TFM2_Taraspina_miTags_analysis
lrubinat
5/23/2017
- 1) 18S amplicons
- 2) 16S amplicons
1) 18S amplicons
1.1) Data overview
The dataset “Taraspina 18S miTags” contains reads from 45 samples of Tara Oceans and from 10 samples of Malaspina. On average, each sample contains 4440 OTUs:
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 93 1840 3086 4440 5808 23780
Overall reads per sample:
1.2) Normalization
In order to keep as many samples as possible, we rarefy at 1154 reads per sample. By that, we loose 10 samples, and after removing the exluded samples in the 16S dataset (to make them comparable), we end up with a normalized dataset containing 43 samples and 5669 OTUs.
Datasets summary:
dim(tb18_tax) #original dataset## [1] 8642 57dim(tb18_tax_occur) #original dataset with occurrence data alone## [1] 8642 55dim(tb18_tax_occur_min1154) #dataset without samples with less than 1154 OTUs## [1] 8349 43dim(tb18_tax_occur_ss1154_no_cero) #rarefied dataset## [1] 43 56841.3) General community analysis
1.3.1) Richness and evenness (Shannon index)
Most of the samples take Shannon Index values around 6:
1.3.2) Richness: OTU number
Lowest number of OTUs per sample:
## [1] 353Maximum number of OTUs per sample:
## [1] 807In most of the samples, we can identify between 600 and 700 OTUs:
1.3.3) Index of evenness
1.3.3.1) Pielou’s index
The Pielou index (constrained between 0 and 1) takes values closer to 1 as the variation of species proportion in a sample increases. Most of the samples get values between 0.90 and 0.95, meaning that the numerical composition of different OTUs in a sample is highly variable - there’s no constant presence of dominant species.
1.3.4) Abundance Models
Most of the OTUs show very few occurrences, suggesting that we will probably be able to identify a significant ammount of rare otus:
1.3.4.1) Rank-Abundance or Dominance/Diversity Model (“radfit”)
The OTUs abundance distribution fits relativelly close to log-normal model.
1.3.4.2) Preston’s Log-normal Model
According to Preston’s lognormal model fitted into groups of species’ frequencies, we’re missing 1588.816 species:
## Extrapolated Observed Veiled
## 9937.816 8349.000 1588.816
When computing Prestons’ lognormal model fit without pooling data into groups, we miss 1385.371 species:
## Extrapolated Observed Veiled
## 9734.371 8349.000 1385.3711.3.5) Rarefaction curves of rarefied and non-rarefied datasets
1.3.6) Beta diversity
1.3.6.1) Dissimilarity matrix using Bray-Curtis index:
The Bray-Curtis dissimilarity, constrained between 0 (minimum distance) and 1 (highest dissimilarity) allows us to quantify the differences between samples according to the composition and the relative abundance of their OTUs. In our dataset, most of the samples pairs take dissimilarity values around 0.8, meaning that their composition is substantially different.
1.3.6.2) Hierarchical clustering
The stations seem to form clusters according to geographic localization, but there are no evident clusters separated from the general groups, apart from the one containing TARA_84, TARA_82 and TARA_85.
(To be done: assign Longhurst provinces information to each station and check if any of the central clusters is meaningful regarding to the samples’ geographical location)
1.3.6.3) Non-metric multidimensional scaling
We can identify a prominent group in the central part of the NMDS plot and a few outliers (TARA 82, 84 and 85) in the central-right edge of the plot. The stress parameter takes a value below 0.2, suggesting that the plot is acceptable.
##
## Call:
## monoMDS(dist = tb18_tax_occur_ss1154_no_cero.bray)
##
## Non-metric Multidimensional Scaling
##
## 43 points, dissimilarity 'bray', call 'vegdist(x = tb18_tax_occur_ss1154_no_cero, method = "bray")'
##
## Dimensions: 2
## Stress: 0.1397828
## Stress type 1, weak ties
## Scores scaled to unit root mean square, rotated to principal components
## Stopped after 55 iterations: Stress nearly unchanged (ratio > sratmax)
1.4) Geographical analysis
Communities quickly change their composition across geographical distances:
1.4.1) Mantel correlograms
Mantel statistic is -significantlly- so low, meaning that the correlation between samples dissimilarity and geographical distances is weak.
##
## Mantel statistic based on Pearson's product-moment correlation
##
## Call:
## mantel(xdis = geo_distances_MP_18S, ydis = tb18_tax_occur_ss1154_no_cero.bray)
##
## Mantel statistic r: 0.1237
## Significance: 0.013
##
## Upper quantiles of permutations (null model):
## 90% 95% 97.5% 99%
## 0.0671 0.0866 0.1087 0.1275
## Permutation: free
## Number of permutations: 999Correlograms:
MP_18s_ss1154_mantel_correl_by_1000km<-mantel.correlog(tb18_tax_occur_ss1154_no_cero.bray, D.geo=geo_distances_MP_18S, break.pts=seq(0,20000, by=1000))
plot(MP_18s_ss1154_mantel_correl_by_1000km)
MP_18s_ss1154_mantel_correl_by_100km<-mantel.correlog(tb18_tax_occur_ss1154_no_cero.bray, D.geo=geo_distances_MP_18S, break.pts=seq(0,20000, by=100))
plot(MP_18s_ss1154_mantel_correl_by_100km)
1.5) Abundance vs. occurence
OTUs distribution according to their percentage of occurence and relative abundance.
- red line: OTUs that occur in more than 80% of the samples.
- blue line: regionally abundant OTUs (> 0.1%).
Regionally abundant OTUs (relative abundance over 0.1%):
## otu_names mean_rabund perc_occur classif
## 93 OTU_38 0.017451937 90.697674 Pelagophyceae
## 88 OTU_3677 0.014187256 79.069767 Prymnesiophyceae
## 126 OTU_751 0.010640442 39.534884 Prasinophyceae_clade-VII
## 116 OTU_5415 0.010237395 25.581395 <NA>
## 81 OTU_3374 0.008484140 86.046512 Pelagophyceae
## 50 OTU_2494 0.007113780 72.093023 Prymnesiophyceae
## 55 OTU_2631 0.005783725 72.093023 Prymnesiophyceae
## 76 OTU_3177 0.005763573 46.511628 Mamiellophyceae
## 85 OTU_3569 0.005300069 46.511628 Mamiellophyceae
## 4 OTU_1032 0.005118697 69.767442 Prymnesiophyceae
## 134 OTU_933 0.004796260 95.348837 Prymnesiophyceae
## 80 OTU_3282 0.004735803 46.511628 Mamiellophyceae
## 89 OTU_3729 0.004272299 76.744186 Pelagophyceae
## 115 OTU_5120 0.004111080 39.534884 Mamiellophyceae
## 65 OTU_2910 0.003990166 74.418605 <NA>
## 104 OTU_4144 0.003949861 46.511628 Mamiellophyceae
## 41 OTU_2200 0.003768490 90.697674 <NA>
## 83 OTU_3454 0.003587119 76.744186 <NA>
## 26 OTU_1921 0.003546814 86.046512 Prymnesiophyceae
## 78 OTU_3227 0.003425900 34.883721 Prasinophyceae_clade-VII
## 16 OTU_1597 0.003304986 83.720930 Prymnesiophyceae
## 105 OTU_4176 0.003264681 32.558140 Mamiellophyceae
## 109 OTU_4227 0.003244529 32.558140 Prasinophyceae_clade-VII
## 101 OTU_4123 0.003123615 39.534884 Prasinophyceae_clade-VII
## 72 OTU_3038 0.003103462 81.395349 <NA>
## 10 OTU_1383 0.003083310 81.395349 <NA>
## 13 OTU_1456 0.002942243 83.720930 Dinophyceae
## 141 OTU_974 0.002922091 65.116279 Prymnesiophyceae
## 23 OTU_1833 0.002781025 83.720930 <NA>
## 132 OTU_896 0.002720567 72.093023 <NA>
## 102 OTU_4125 0.002519044 81.395349 Pelagophyceae
## 99 OTU_4103 0.002418282 39.534884 Mamiellophyceae
## 70 OTU_2996 0.002377978 62.790698 <NA>
## 30 OTU_2031 0.002337673 62.790698 <NA>
## 138 OTU_950 0.002216759 4.651163 Prymnesiophyceae
## 79 OTU_3271 0.002196606 30.232558 Prasinophyceae_clade-VII
## 96 OTU_3926 0.002156302 62.790698 Pelagophyceae
## 95 OTU_3871 0.002136149 72.093023 <NA>
## 103 OTU_4134 0.002075692 53.488372 Pelagophyceae
## 112 OTU_4518 0.002075692 37.209302 Mamiellophyceae
## 137 OTU_949 0.002055540 60.465116 Dictyochophyceae
## 84 OTU_3560 0.001954778 65.116279 Pelagophyceae
## 52 OTU_2553 0.001954778 81.395349 <NA>
## 131 OTU_893 0.001934626 53.488372 <NA>
## 45 OTU_2305 0.001874169 72.093023 <NA>
## 3 OTU_1018 0.001833864 11.627907 Prymnesiophyceae
## 43 OTU_2269 0.001813712 81.395349 <NA>
## 5 OTU_1047 0.001813712 67.441860 <NA>
## 62 OTU_2868 0.001813712 53.488372 <NA>
## 98 OTU_4090 0.001773407 30.232558 Mamiellophyceae
## 53 OTU_256 0.001733102 72.093023 <NA>
## 125 OTU_717 0.001733102 67.441860 Dinophyceae
## 57 OTU_2654 0.001712950 69.767442 Pelagophyceae
## 108 OTU_4226 0.001712950 41.860465 Mamiellophyceae
## 21 OTU_1746 0.001692798 72.093023 Prymnesiophyceae
## 110 OTU_4260 0.001692798 46.511628 Mamiellophyceae
## 11 OTU_1395 0.001692798 20.930233 <NA>
## 94 OTU_380 0.001672645 83.720930 Prymnesiophyceae
## 18 OTU_1635 0.001672645 74.418605 <NA>
## 75 OTU_3124 0.001652493 65.116279 <NA>
## 9 OTU_1343 0.001632340 69.767442 Dinophyceae
## 31 OTU_2043 0.001612188 60.465116 <NA>
## 127 OTU_758 0.001612188 60.465116 <NA>
## 130 OTU_884 0.001531579 81.395349 <NA>
## 38 OTU_216 0.001531579 62.790698 Dinophyceae
## 140 OTU_973 0.001531579 62.790698 <NA>
## 117 OTU_5484 0.001511426 34.883721 Mamiellophyceae
## 58 OTU_2686 0.001491274 74.418605 <NA>
## 19 OTU_1641 0.001491274 72.093023 Dinophyceae
## 40 OTU_2195 0.001491274 72.093023 Dinophyceae
## 64 OTU_2887 0.001491274 69.767442 <NA>
## 71 OTU_3018 0.001491274 67.441860 <NA>
## 87 OTU_363 0.001491274 60.465116 <NA>
## 67 OTU_2965 0.001491274 58.139535 <NA>
## 113 OTU_4533 0.001450969 44.186047 Mamiellophyceae
## 42 OTU_2207 0.001450969 79.069767 Dinophyceae
## 32 OTU_2078 0.001450969 72.093023 <NA>
## 51 OTU_2518 0.001410665 55.813953 <NA>
## 59 OTU_2730 0.001390512 60.465116 <NA>
## 107 OTU_4203 0.001390512 55.813953 Pelagophyceae
## 133 OTU_914 0.001370360 67.441860 Prymnesiophyceae
## 97 OTU_4089 0.001370360 37.209302 Mamiellophyceae
## 56 OTU_2648 0.001350208 79.069767 <NA>
## 20 OTU_1694 0.001330055 67.441860 <NA>
## 74 OTU_3056 0.001330055 65.116279 <NA>
## 2 OTU_1012 0.001309903 65.116279 <NA>
## 47 OTU_2429 0.001289751 74.418605 Prymnesiophyceae
## 128 OTU_793 0.001289751 74.418605 <NA>
## 86 OTU_3602 0.001289751 62.790698 <NA>
## 54 OTU_2594 0.001289751 58.139535 <NA>
## 28 OTU_1997 0.001269598 81.395349 Prymnesiophyceae
## 12 OTU_1446 0.001269598 65.116279 <NA>
## 122 OTU_6181 0.001269598 23.255814 <NA>
## 123 OTU_628 0.001249446 60.465116 Dinophyceae
## 35 OTU_2120 0.001249446 58.139535 <NA>
## 139 OTU_952 0.001249446 53.488372 Dinophyceae
## 124 OTU_6608 0.001249446 23.255814 <NA>
## 119 OTU_584 0.001249446 11.627907 <NA>
## 27 OTU_1929 0.001229293 44.186047 Mamiellophyceae
## 114 OTU_458 0.001209141 60.465116 Prymnesiophyceae
## 1 OTU_1001 0.001209141 53.488372 <NA>
## 6 OTU_1066 0.001209141 44.186047 Prymnesiophyceae
## 44 OTU_2284 0.001188989 53.488372 <NA>
## 73 OTU_3055 0.001188989 53.488372 Chrysophyceae
## 49 OTU_2466 0.001188989 51.162791 <NA>
## 33 OTU_2086 0.001148684 58.139535 Dinophyceae
## 142 OTU_990 0.001148684 58.139535 <NA>
## 39 OTU_2189 0.001148684 53.488372 <NA>
## 82 OTU_3430 0.001148684 30.232558 Mamiellophyceae
## 61 OTU_2853 0.001148684 74.418605 Prymnesiophyceae
## 14 OTU_1496 0.001128532 72.093023 <NA>
## 111 OTU_437 0.001128532 67.441860 Prymnesiophyceae
## 91 OTU_3751 0.001128532 48.837209 <NA>
## 15 OTU_1551 0.001108379 67.441860 <NA>
## 120 OTU_599 0.001108379 65.116279 <NA>
## 69 OTU_2986 0.001108379 60.465116 <NA>
## 77 OTU_3196 0.001108379 60.465116 Prymnesiophyceae
## 37 OTU_2158 0.001108379 58.139535 Prymnesiophyceae
## 7 OTU_1087 0.001108379 55.813953 <NA>
## 135 OTU_936 0.001088227 53.488372 <NA>
## 129 OTU_825 0.001088227 48.837209 <NA>
## 66 OTU_2916 0.001088227 46.511628 <NA>
## 17 OTU_1628 0.001068075 65.116279 Dinophyceae
## 25 OTU_1902 0.001068075 58.139535 Prymnesiophyceae
## 34 OTU_2089 0.001068075 53.488372 <NA>
## 100 OTU_4115 0.001068075 51.162791 <NA>
## 60 OTU_2811 0.001047922 46.511628 <NA>
## 92 OTU_3754 0.001047922 46.511628 <NA>
## 22 OTU_1825 0.001027770 55.813953 <NA>
## 90 OTU_373 0.001027770 55.813953 <NA>
## 63 OTU_2873 0.001027770 53.488372 <NA>
## 106 OTU_4190 0.001027770 30.232558 Mamiellophyceae
## 118 OTU_5496 0.001027770 9.302326 <NA>
## 136 OTU_938 0.001007618 65.116279 <NA>
## 36 OTU_2124 0.001007618 62.790698 Dictyochophyceae
## 8 OTU_1261 0.001007618 60.465116 <NA>
## 68 OTU_2966 0.001007618 60.465116 <NA>
## 46 OTU_2365 0.001007618 53.488372 <NA>
## 48 OTU_2453 0.001007618 53.488372 <NA>
## 121 OTU_6 0.001007618 44.186047 <NA>
## 29 OTU_2030 0.001007618 55.813953 <NA>
## 24 OTU_1879 0.001007618 48.837209 Prymnesiophyceae
## OTUId
## 93 SILVA.v123_KF130487.1.1773_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;uncultured_eukaryote
## 88 SILVA.v123_X77478.1.1803_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;Phaeocystis_antarctica
## 126 SILVA.v123_KJ760716.1.1777_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Clade_VII;Subclade_B;uncultured_eukaryote
## 116 SILVA.v123_AF315604.1.1807_Eukaryota;SAR;Stramenopiles;Bicosoecida;Pseudobodo;Pseudobodo_tremulans
## 81 SILVA.v123_AC236360.17941.19743_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;Aureococcus;Aureococcus_anophagefferens
## 50 SILVA.v123_KF422607.1.1694_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;Haptophyceae_sp._CCMP2000
## 55 SILVA.v123_AJ278037.1.1602_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;Phaeocystis_globosa
## 76 SILVA.v123_FR874477.1.1775_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Bathycoccus;uncultured_marine_picoeukaryote
## 85 SILVA.v123_FR874422.1.1776_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Bathycoccus;uncultured_marine_picoeukaryote
## 4 SILVA.v123_AY851300.1.1802_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;Phaeocystis_globosa
## 134 SILVA.v123_KJ763007.1.1798_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_eukaryote
## 80 SILVA.v123_AACY020218946.53.1575_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Ostreococcus;marine_metagenome
## 89 SILVA.v123_ACJI01001310.5359.7147_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;Aureococcus;Aureococcus_anophagefferens
## 115 SILVA.v123_KJ763259.1.1763_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Ostreococcus;uncultured_eukaryote
## 65 SILVA.v123_KJ763800.1.1807_Eukaryota;DH147_EKD10;uncultured_eukaryote
## 104 SILVA.v123_FR874693.1.1777_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Bathycoccus;uncultured_marine_picoeukaryote
## 41 SILVA.v123_KF130192.1.1763_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;uncultured_eukaryote
## 83 SILVA.v123_KJ763934.1.1796_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 26 SILVA.v123_HM581633.1.1797_Eukaryota;Haptophyta;Prymnesiophyceae;OLI16010;uncultured_marine_eukaryote
## 78 SILVA.v123_FJ537298.1.1778_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Clade_VII;Subclade_B;uncultured_Prasinophyceae
## 16 SILVA.v123_KJ762902.1.1800_Eukaryota;Haptophyta;Prymnesiophyceae;OLI16010;uncultured_eukaryote
## 105 SILVA.v123_AF525858.1.1766_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Ostreococcus;uncultured_marine_eukaryote
## 109 SILVA.v123_FJ537306.1.1756_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Clade_VII;Subclade_B;uncultured_Prasinophyceae
## 101 SILVA.v123_KF031720.1.1747_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Clade_VII;Subclade_B;uncultured_eukaryote
## 72 SILVA.v123_KJ763586.1.1789_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 10 SILVA.v123_KJ763777.1.1804_Eukaryota;SAR;Alveolata;NIF_4C10;uncultured_eukaryote
## 13 SILVA.v123_KJ763154.1.1799_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;SCM15C35;uncultured_eukaryote
## 141 SILVA.v123_KF620996.1.1754_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_haptophyte
## 23 SILVA.v123_JQ781940.1.1785_Eukaryota;SAR;Stramenopiles;MAST_1;MAST_1D;uncultured_stramenopile
## 132 SILVA.v123_KJ763301.1.1788_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 102 SILVA.v123_JN934690.1.1635_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Sarcinochrysidales;Ankylochrisis;Pelagophyceae_sp._RCC2505
## 99 SILVA.v123_AACY023218795.1.1233_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Bathycoccus;marine_metagenome
## 70 SILVA.v123_KF130265.1.1745_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 30 SILVA.v123_KC488619.1.1713_Eukaryota;Incertae_Sedis;Telonema;uncultured_Telonemida
## 138 SILVA.v123_KF130149.1.1755_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;Braarudosphaera;uncultured_eukaryote
## 79 SILVA.v123_AJ402359.1.1758_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Clade_VII;Subclade_B;eukaryote_clone_OLI11345
## 96 SILVA.v123_U40257.1.1813_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;Aureococcus;Aureococcus_anophagefferens
## 95 SILVA.v123_KJ760785.1.1797_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 103 SILVA.v123_JQ420078.1.1796_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;Aureococcus;Aureococcus_anophagefferens
## 112 SILVA.v123_KC583088.1.1775_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Micromonas;uncultured_Chlorophyta
## 137 SILVA.v123_KJ759450.1.1797_Eukaryota;SAR;Stramenopiles;Ochrophyta;Dictyochophyceae;uncultured_eukaryote
## 84 SILVA.v123_KC488601.1.1695_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;uncultured_stramenopile
## 52 SILVA.v123_KJ759432.1.1798_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;uncultured_eukaryote
## 131 SILVA.v123_EU793380.1.1676_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_syndiniales
## 45 SILVA.v123_EU793930.1.1664_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_syndiniales
## 3 SILVA.v123_KJ763100.1.1794_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;Braarudosphaera;uncultured_eukaryote
## 43 SILVA.v123_KJ763285.1.1791_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 5 SILVA.v123_EF173010.1.1664_Eukaryota;SAR;Stramenopiles;MAST_1;MAST_1D;uncultured_eukaryote
## 62 SILVA.v123_KF129704.1.1753_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 98 SILVA.v123_AF525854.1.1776_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Micromonas;uncultured_marine_eukaryote
## 53 SILVA.v123_KJ763667.1.1784_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 125 SILVA.v123_KJ759460.1.1796_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;Gymnodiniphycidae;Kareniaceae;Karlodinium;uncultured_eukaryote
## 57 SILVA.v123_KJ763141.1.1812_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;uncultured_eukaryote
## 108 SILVA.v123_AY955007.1.1727_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Micromonas;Micromonas_pusilla
## 21 SILVA.v123_KF620989.1.1797_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_haptophyte
## 110 SILVA.v123_KF130557.1.1738_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Micromonas;uncultured_eukaryote
## 11 SILVA.v123_DQ310274.1.1563_Eukaryota;SAR;Stramenopiles;Bicosoecida;Pseudobodo;uncultured_marine_eukaryote
## 94 SILVA.v123_KC488456.1.1659_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;OLI16029;uncultured_haptophyte
## 18 SILVA.v123_KJ759387.1.1799_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;uncultured_eukaryote
## 75 SILVA.v123_KJ763702.1.1796_Eukaryota;SAR;Rhizaria;Retaria;RAD_A;uncultured_eukaryote
## 9 SILVA.v123_KJ763402.1.1791_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;B7;uncultured_eukaryote
## 31 SILVA.v123_KJ760589.1.1792_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 127 SILVA.v123_KF130519.1.1757_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 130 SILVA.v123_KF129962.1.1754_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 38 SILVA.v123_KJ762854.1.1799_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;SCM15C35;uncultured_eukaryote
## 140 SILVA.v123_KJ759337.1.1800_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;uncultured_eukaryote
## 117 SILVA.v123_FR874326.1.1777_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;uncultured_marine_picoeukaryote
## 58 SILVA.v123_KF130465.1.1754_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 19 SILVA.v123_KJ763566.1.1798_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;B36;uncultured_eukaryote
## 40 SILVA.v123_KJ759410.1.1799_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;Gymnodiniphycidae;Gyrodinium;uncultured_eukaryote
## 64 SILVA.v123_GU823185.1.1396_Eukaryota;SAR;Stramenopiles;MAST_4;MAST_4F;uncultured_stramenopile
## 71 SILVA.v123_KC488464.1.1700_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;uncultured_marine_alveolate
## 87 SILVA.v123_AJ402349.1.1758_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;eukaryote_clone_OLI11005
## 67 SILVA.v123_KF130546.1.1757_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 113 SILVA.v123_FJ537303.1.1776_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Micromonas;uncultured_Micromonas
## 42 SILVA.v123_KJ763882.1.1802_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;SL163A10;uncultured_eukaryote
## 32 SILVA.v123_KJ762856.1.1793_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 51 SILVA.v123_KJ763625.1.1800_Eukaryota;SAR;Alveolata;SCM37C52;uncultured_eukaryote
## 59 SILVA.v123_KJ759527.1.1799_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 107 SILVA.v123_JF794050.1.1619_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Sarcinochrysidales;Ankylochrisis;Pelagophyceae_sp._RCC2040
## 133 SILVA.v123_AM779755.1.1802_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;Prymnesium;Prymnesium_palpebrale
## 97 SILVA.v123_HM581768.1.1760_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Micromonas;uncultured_marine_eukaryote
## 56 SILVA.v123_KJ763500.1.1801_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 20 SILVA.v123_JX188383.1.1765_Eukaryota;Picozoa;Picomonadida;uncultured_eukaryote
## 74 SILVA.v123_KJ763348.1.1800_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 2 SILVA.v123_JQ781943.1.1807_Eukaryota;SAR;Stramenopiles;MAST_4;MAST_4F;uncultured_stramenopile
## 47 SILVA.v123_DQ369019.1.1798_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;OLI16029;uncultured_marine_eukaryote
## 128 SILVA.v123_KJ759134.1.1789_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 86 SILVA.v123_KJ759592.1.1801_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 54 SILVA.v123_KC488339.1.1675_Eukaryota;Picozoa;Picomonadida;uncultured_biliphyte
## 28 SILVA.v123_KJ760407.1.1804_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_eukaryote
## 12 SILVA.v123_KJ759482.1.1801_Eukaryota;SAR;Stramenopiles;Ochrophyta;MOCH_2;uncultured_eukaryote
## 122 SILVA.v123_FR874360.1.1745_Eukaryota;SAR;Alveolata;Ciliophora;Intramacronucleata;Spirotrichea;Choreotrichia;uncultured;uncultured_marine_picoeukaryote
## 123 SILVA.v123_KC582936.1.1795_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;Gymnodiniphycidae;SCM27C9;uncultured_alveolate
## 35 SILVA.v123_JF826343.1.1605_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_marine_alveolate
## 139 SILVA.v123_KJ763684.1.1796_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;Gymnodiniphycidae;Kareniaceae;Karlodinium;uncultured_eukaryote
## 124 SILVA.v123_KJ760788.1.1795_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 119 SILVA.v123_AF280076.1.1787_Eukaryota;SAR;Alveolata;Protalveolata;Colpodellida;Voromonas;Voromonas_pontica
## 27 SILVA.v123_KJ763184.1.1781_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Ostreococcus;uncultured_eukaryote
## 114 SILVA.v123_GQ863817.1.1709_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_eukaryote
## 1 SILVA.v123_KJ759516.1.1803_Eukaryota;SAR;Stramenopiles;Ochrophyta;MOCH_2;uncultured_eukaryote
## 6 SILVA.v123_AF180940.1.1800_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;Phaeocystis_sp._PLY559
## 44 SILVA.v123_KF129645.1.1757_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 73 SILVA.v123_AY129063.1.1782_Eukaryota;SAR;Stramenopiles;Ochrophyta;Chrysophyceae;E222;uncultured_marine_eukaryote
## 49 SILVA.v123_JF790988.1.1777_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;Karlodinium_veneficum
## 33 SILVA.v123_GU820601.1.1201_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;Gymnodiniphycidae;Kareniaceae;Karlodinium;uncultured_dinoflagellate
## 142 SILVA.v123_JF826317.1.1608_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_marine_alveolate
## 39 SILVA.v123_KC488461.1.1687_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_marine_alveolate
## 82 SILVA.v123_GQ863805.1.1662_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Micromonas;uncultured_eukaryote
## 61 SILVA.v123_KJ762999.1.1800_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;uncultured_eukaryote
## 14 SILVA.v123_KJ759353.1.1798_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 111 SILVA.v123_KF129692.1.1759_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;uncultured_eukaryote
## 91 SILVA.v123_JQ781985.1.1807_Eukaryota;SAR;Stramenopiles;MAST_11;uncultured_stramenopile
## 15 SILVA.v123_KJ762893.1.1791_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 120 SILVA.v123_KJ759333.1.1794_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 69 SILVA.v123_KC582982.1.1806_Eukaryota;SAR;Stramenopiles;MAST_4;MAST_4F;uncultured_stramenopile
## 77 SILVA.v123_KF129663.1.1757_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;OLI16029;uncultured_eukaryote
## 37 SILVA.v123_AF107080.1.1795_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;OLI16029;unidentified_prymnesiophyte_clone_OLI16029
## 7 SILVA.v123_KF031588.1.1755_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 135 SILVA.v123_JX188306.1.1756_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_V;uncultured_eukaryote
## 129 SILVA.v123_JQ782001.1.1776_Eukaryota;SAR;Stramenopiles;MAST_1;MAST_1B;uncultured_stramenopile
## 66 SILVA.v123_KC582940.1.1794_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_alveolate
## 17 SILVA.v123_KJ763683.1.1799_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;B36;uncultured_eukaryote
## 25 SILVA.v123_KF130516.1.1755_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;OLI51059;uncultured_eukaryote
## 34 SILVA.v123_KJ759300.1.1793_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_V;uncultured_eukaryote
## 100 SILVA.v123_KJ760584.1.1798_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 60 SILVA.v123_KF130084.1.1751_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 92 SILVA.v123_KJ760745.1.1794_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 22 SILVA.v123_KF130023.1.1761_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 90 SILVA.v123_KJ760345.1.1797_Eukaryota;SAR;Alveolata;SCM37C52;uncultured_eukaryote
## 63 SILVA.v123_JQ781946.1.1806_Eukaryota;SAR;Stramenopiles;MAST_4;uncultured_stramenopile
## 106 SILVA.v123_KJ762855.1.1768_Eukaryota;Archaeplastida;Chloroplastida;Chlorophyta;Mamiellophyceae;Mamiellales;Ostreococcus;uncultured_eukaryote
## 118 SILVA.v123_KJ762455.1.1745_Eukaryota;SAR;Alveolata;Ciliophora;Intramacronucleata;Spirotrichea;Choreotrichia;uncultured;uncultured_eukaryote
## 136 SILVA.v123_KF129758.1.1746_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 36 SILVA.v123_KC488605.1.1648_Eukaryota;SAR;Stramenopiles;Ochrophyta;Dictyochophyceae;Dictyochales;Florenciella;uncultured_stramenopile
## 8 SILVA.v123_KJ760603.1.1795_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 68 SILVA.v123_JQ782044.1.1803_Eukaryota;SAR;Stramenopiles;MAST_4;uncultured_stramenopile
## 46 SILVA.v123_GQ365865.1.1537_Eukaryota;Incertae_Sedis;Telonema;uncultured_eukaryote
## 48 SILVA.v123_KJ759424.1.1796_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_II;uncultured_eukaryote
## 121 SILVA.v123_KF031747.1.1743_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 29 SILVA.v123_KJ759570.1.1784_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 24 SILVA.v123_KF620977.1.1797_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_haptophyteNumber and roportion of regionally abundant OTUs (%):
## [1] 142## [1] 2.498241
Cosmopolitan OTUs (relative abundance over 0.1% and occurence in more than 80% of samples):
## otu_names mean_rabund perc_occur classif
## 16 OTU_933 0.004796260 95.34884 Prymnesiophyceae
## 12 OTU_38 0.017451937 90.69767 Pelagophyceae
## 7 OTU_2200 0.003768490 90.69767 <NA>
## 11 OTU_3374 0.008484140 86.04651 Pelagophyceae
## 5 OTU_1921 0.003546814 86.04651 Prymnesiophyceae
## 3 OTU_1597 0.003304986 83.72093 Prymnesiophyceae
## 2 OTU_1456 0.002942243 83.72093 Dinophyceae
## 4 OTU_1833 0.002781025 83.72093 <NA>
## 13 OTU_380 0.001672645 83.72093 Prymnesiophyceae
## 10 OTU_3038 0.003103462 81.39535 <NA>
## 1 OTU_1383 0.003083310 81.39535 <NA>
## 14 OTU_4125 0.002519044 81.39535 Pelagophyceae
## 9 OTU_2553 0.001954778 81.39535 <NA>
## 8 OTU_2269 0.001813712 81.39535 <NA>
## 15 OTU_884 0.001531579 81.39535 <NA>
## 6 OTU_1997 0.001269598 81.39535 Prymnesiophyceae
## OTUId
## 16 SILVA.v123_KJ763007.1.1798_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_eukaryote
## 12 SILVA.v123_KF130487.1.1773_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;uncultured_eukaryote
## 7 SILVA.v123_KF130192.1.1763_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;uncultured_eukaryote
## 11 SILVA.v123_AC236360.17941.19743_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Pelagomonadales;Aureococcus;Aureococcus_anophagefferens
## 5 SILVA.v123_HM581633.1.1797_Eukaryota;Haptophyta;Prymnesiophyceae;OLI16010;uncultured_marine_eukaryote
## 3 SILVA.v123_KJ762902.1.1800_Eukaryota;Haptophyta;Prymnesiophyceae;OLI16010;uncultured_eukaryote
## 2 SILVA.v123_KJ763154.1.1799_Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;SCM15C35;uncultured_eukaryote
## 4 SILVA.v123_JQ781940.1.1785_Eukaryota;SAR;Stramenopiles;MAST_1;MAST_1D;uncultured_stramenopile
## 13 SILVA.v123_KC488456.1.1659_Eukaryota;Haptophyta;Prymnesiophyceae;Prymnesiales;OLI16029;uncultured_haptophyte
## 10 SILVA.v123_KJ763586.1.1789_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 1 SILVA.v123_KJ763777.1.1804_Eukaryota;SAR;Alveolata;NIF_4C10;uncultured_eukaryote
## 14 SILVA.v123_JN934690.1.1635_Eukaryota;SAR;Stramenopiles;Ochrophyta;Pelagophyceae;Sarcinochrysidales;Ankylochrisis;Pelagophyceae_sp._RCC2505
## 9 SILVA.v123_KJ759432.1.1798_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_III;uncultured_eukaryote
## 8 SILVA.v123_KJ763285.1.1791_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 15 SILVA.v123_KF129962.1.1754_Eukaryota;SAR;Alveolata;Protalveolata;Syndiniales;Syndiniales_Group_I;uncultured_eukaryote
## 6 SILVA.v123_KJ760407.1.1804_Eukaryota;Haptophyta;Prymnesiophyceae;Phaeocystis;uncultured_eukaryoteNumber and proportion (%) of cosmopolitan OTUs:
## [1] 16## [1] 0.2814919Number and proportion (%) of rare OTUs:
## [1] 0## [1] 01.6) Taxonomic composition analysis
1.6.1) Normalized data
PHOTOTROPHS + HETEROTROPHS
No. of OTUs and reads of the rearefied dataset:
## [1] 5684## [1] 49622No. of OTUs and reads of phototrophic groups:
## [1] 1895## [1] 20050No. of OTUs and reads of non-phototrophic groups:
## [1] 3789## [1] 29572
Absolute values
## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 297 135 39
## Bolidophyceae 136 21 36
## Chlorarachniophyceae 109 14 28
## Chlorophyceae 22 16 14
## Chrysophyceae 610 133 42
## Cryptophyceae 381 56 26
## Dictyochophyceae 644 47 43
## Dinophyceae 5441 1026 43
## Eustigmatophyceae 96 21 36
## Heterotrophs 29572 3789 43
## Mamiellophyceae 3166 99 37
## Nephroselmidophyceae 18 6 13
## Pavlovophyceae 48 6 25
## Pelagophyceae 2195 21 43
## Phaeophyceae 1 1 1
## Prasinophyceae_clade-IX 63 13 17
## Prasinophyceae_clade-VII 1370 31 38
## Prymnesiophyceae 5192 168 43
## Pyramimonadaceae 100 16 23
## Rhodophyceae 8 7 7
## Trebouxiophyceae 42 30 17
## Ulvophyceae 2 2 2
## Xanthophyceae 4 4 4
## other_Prasinophyceae 105 22 32
Relative values
## reads_per_class OTUs_per_class samples_per_class
## 100.000 100.000 1516.279## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 0.598524848 2.37508797 90.697674
## Bolidophyceae 0.274071984 0.36945813 83.720930
## Chlorarachniophyceae 0.219660634 0.24630542 65.116279
## Chlorophyceae 0.044335174 0.28149191 32.558140
## Chrysophyceae 1.229293459 2.33990148 97.674419
## Cryptophyceae 0.767804603 0.98522167 60.465116
## Dictyochophyceae 1.297811455 0.82688248 100.000000
## Dinophyceae 10.964894603 18.05066854 100.000000
## Eustigmatophyceae 0.193462577 0.36945813 83.720930
## Heterotrophs 59.594534682 66.66080225 100.000000
## Mamiellophyceae 6.380234573 1.74173118 86.046512
## Nephroselmidophyceae 0.036274233 0.10555947 30.232558
## Pavlovophyceae 0.096731289 0.10555947 58.139535
## Pelagophyceae 4.423441216 0.36945813 100.000000
## Phaeophyceae 0.002015235 0.01759324 2.325581
## Prasinophyceae_clade-IX 0.126959816 0.22871217 39.534884
## Prasinophyceae_clade-VII 2.760872194 0.54539057 88.372093
## Prymnesiophyceae 10.463101044 2.95566502 100.000000
## Pyramimonadaceae 0.201523518 0.28149191 53.488372
## Rhodophyceae 0.016121881 0.12315271 16.279070
## Trebouxiophyceae 0.084639877 0.52779733 39.534884
## Ulvophyceae 0.004030470 0.03518649 4.651163
## Xanthophyceae 0.008060941 0.07037298 9.302326
## other_Prasinophyceae 0.211599694 0.38705137 74.418605
Reads per class vs. OTUs per class:
Reads per class vs. samples in which they occurr:
PHOTOTROPHS
Absolute values
## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 297 135 39
## Bolidophyceae 136 21 36
## Chlorarachniophyceae 109 14 28
## Chlorophyceae 22 16 14
## Chrysophyceae 610 133 42
## Cryptophyceae 381 56 26
## Dictyochophyceae 644 47 43
## Dinophyceae 5441 1026 43
## Eustigmatophyceae 96 21 36
## Mamiellophyceae 3166 99 37
## Nephroselmidophyceae 18 6 13
## Pavlovophyceae 48 6 25
## Pelagophyceae 2195 21 43
## Phaeophyceae 1 1 1
## Prasinophyceae_clade-IX 63 13 17
## Prasinophyceae_clade-VII 1370 31 38
## Prymnesiophyceae 5192 168 43
## Pyramimonadaceae 100 16 23
## Rhodophyceae 8 7 7
## Trebouxiophyceae 42 30 17
## Ulvophyceae 2 2 2
## Xanthophyceae 4 4 4
## other_Prasinophyceae 105 22 32
Relative values
## reads_per_class OTUs_per_class samples_per_class
## 100.000 100.000 1416.279## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 1.481296758 7.12401055 90.697674
## Bolidophyceae 0.678304239 1.10817942 83.720930
## Chlorarachniophyceae 0.543640898 0.73878628 65.116279
## Chlorophyceae 0.109725686 0.84432718 32.558140
## Chrysophyceae 3.042394015 7.01846966 97.674419
## Cryptophyceae 1.900249377 2.95514512 60.465116
## Dictyochophyceae 3.211970075 2.48021108 100.000000
## Dinophyceae 27.137157107 54.14248021 100.000000
## Eustigmatophyceae 0.478802993 1.10817942 83.720930
## Mamiellophyceae 15.790523691 5.22427441 86.046512
## Nephroselmidophyceae 0.089775561 0.31662269 30.232558
## Pavlovophyceae 0.239401496 0.31662269 58.139535
## Pelagophyceae 10.947630923 1.10817942 100.000000
## Phaeophyceae 0.004987531 0.05277045 2.325581
## Prasinophyceae_clade-IX 0.314214464 0.68601583 39.534884
## Prasinophyceae_clade-VII 6.832917706 1.63588391 88.372093
## Prymnesiophyceae 25.895261845 8.86543536 100.000000
## Pyramimonadaceae 0.498753117 0.84432718 53.488372
## Rhodophyceae 0.039900249 0.36939314 16.279070
## Trebouxiophyceae 0.209476309 1.58311346 39.534884
## Ulvophyceae 0.009975062 0.10554090 4.651163
## Xanthophyceae 0.019950125 0.21108179 9.302326
## other_Prasinophyceae 0.523690773 1.16094987 74.418605
Reads per class vs. OTUs per class:
Reads per class vs. samples in which they occurr:
1.6.2) Non-rarefied data
PHOTOTROPHS + HETEROTROPHS
No. of OTUs and reads of the rearefied dataset:
## [1] 8349## [1] 223622No. of OTUs and reads of phototrophic groups:
## [1] 2882## [1] 100242No. of OTUs and reads of non-phototrophic groups:
## [1] 5467## [1] 123380
Absolute values
## reads_per_class OTUs_per_class
## Bacillariophyceae 2664 374
## Bolidophyceae 509 25
## Chlorarachniophyceae 327 20
## Chlorophyceae 79 45
## Chrysophyceae 2824 240
## Cryptophyceae 1922 95
## Dictyochophyceae 2819 52
## Dinophyceae 23637 1476
## Eustigmatophyceae 359 27
## Heterotrophs 123380 5467
## IncertaeSedis_Archaeplastida 1 1
## Mamiellophyceae 15846 117
## Nephroselmidophyceae 64 7
## Pavlovophyceae 228 13
## Pelagophyceae 9306 25
## Phaeophyceae 5 4
## Phaeothamniophyceae 1 1
## Prasinophyceae_clade-IX 155 16
## Prasinophyceae_clade-VII 3575 37
## Prymnesiophyceae 34758 177
## Pyramimonadaceae 507 19
## Rhodophyceae 16 12
## Trebouxiophyceae 121 57
## Ulvophyceae 6 5
## Xanthophyceae 21 11
## other_Prasinophyceae 492 26
## samples_per_class
## Bacillariophyceae 42
## Bolidophyceae 43
## Chlorarachniophyceae 41
## Chlorophyceae 26
## Chrysophyceae 43
## Cryptophyceae 39
## Dictyochophyceae 43
## Dinophyceae 43
## Eustigmatophyceae 42
## Heterotrophs 43
## IncertaeSedis_Archaeplastida 1
## Mamiellophyceae 41
## Nephroselmidophyceae 19
## Pavlovophyceae 37
## Pelagophyceae 43
## Phaeophyceae 4
## Phaeothamniophyceae 1
## Prasinophyceae_clade-IX 29
## Prasinophyceae_clade-VII 42
## Prymnesiophyceae 43
## Pyramimonadaceae 33
## Rhodophyceae 13
## Trebouxiophyceae 26
## Ulvophyceae 3
## Xanthophyceae 14
## other_Prasinophyceae 41
Relative values
## reads_per_class OTUs_per_class samples_per_class
## 100.000 100.000 1848.837## reads_per_class OTUs_per_class
## Bacillariophyceae 1.191296e+00 4.47957839
## Bolidophyceae 2.276162e-01 0.29943706
## Chlorarachniophyceae 1.462289e-01 0.23954965
## Chlorophyceae 3.532747e-02 0.53898670
## Chrysophyceae 1.262845e+00 2.87459576
## Cryptophyceae 8.594861e-01 1.13786082
## Dictyochophyceae 1.260609e+00 0.62282908
## Dinophyceae 1.057007e+01 17.67876392
## Eustigmatophyceae 1.605388e-01 0.32339202
## Heterotrophs 5.517346e+01 65.48089592
## IncertaeSedis_Archaeplastida 4.471832e-04 0.01197748
## Mamiellophyceae 7.086065e+00 1.40136543
## Nephroselmidophyceae 2.861972e-02 0.08384238
## Pavlovophyceae 1.019578e-01 0.15570727
## Pelagophyceae 4.161487e+00 0.29943706
## Phaeophyceae 2.235916e-03 0.04790993
## Phaeothamniophyceae 4.471832e-04 0.01197748
## Prasinophyceae_clade-IX 6.931339e-02 0.19163972
## Prasinophyceae_clade-VII 1.598680e+00 0.44316685
## Prymnesiophyceae 1.554319e+01 2.12001437
## Pyramimonadaceae 2.267219e-01 0.22757216
## Rhodophyceae 7.154931e-03 0.14372979
## Trebouxiophyceae 5.410917e-02 0.68271649
## Ulvophyceae 2.683099e-03 0.05988741
## Xanthophyceae 9.390847e-03 0.13175231
## other_Prasinophyceae 2.200141e-01 0.31141454
## samples_per_class
## Bacillariophyceae 97.674419
## Bolidophyceae 100.000000
## Chlorarachniophyceae 95.348837
## Chlorophyceae 60.465116
## Chrysophyceae 100.000000
## Cryptophyceae 90.697674
## Dictyochophyceae 100.000000
## Dinophyceae 100.000000
## Eustigmatophyceae 97.674419
## Heterotrophs 100.000000
## IncertaeSedis_Archaeplastida 2.325581
## Mamiellophyceae 95.348837
## Nephroselmidophyceae 44.186047
## Pavlovophyceae 86.046512
## Pelagophyceae 100.000000
## Phaeophyceae 9.302326
## Phaeothamniophyceae 2.325581
## Prasinophyceae_clade-IX 67.441860
## Prasinophyceae_clade-VII 97.674419
## Prymnesiophyceae 100.000000
## Pyramimonadaceae 76.744186
## Rhodophyceae 30.232558
## Trebouxiophyceae 60.465116
## Ulvophyceae 6.976744
## Xanthophyceae 32.558140
## other_Prasinophyceae 95.348837
Reads per class vs. OTUs per class:
Reads per class vs. samples in which they occurr:
PHOTOTROPHS
Absolute values
## reads_per_class OTUs_per_class
## Bacillariophyceae 2664 374
## Bolidophyceae 509 25
## Chlorarachniophyceae 327 20
## Chlorophyceae 79 45
## Chrysophyceae 2824 240
## Cryptophyceae 1922 95
## Dictyochophyceae 2819 52
## Dinophyceae 23637 1476
## Eustigmatophyceae 359 27
## IncertaeSedis_Archaeplastida 1 1
## Mamiellophyceae 15846 117
## Nephroselmidophyceae 64 7
## Pavlovophyceae 228 13
## Pelagophyceae 9306 25
## Phaeophyceae 5 4
## Phaeothamniophyceae 1 1
## Prasinophyceae_clade-IX 155 16
## Prasinophyceae_clade-VII 3575 37
## Prymnesiophyceae 34758 177
## Pyramimonadaceae 507 19
## Rhodophyceae 16 12
## Trebouxiophyceae 121 57
## Ulvophyceae 6 5
## Xanthophyceae 21 11
## other_Prasinophyceae 492 26
## samples_per_class
## Bacillariophyceae 42
## Bolidophyceae 43
## Chlorarachniophyceae 41
## Chlorophyceae 26
## Chrysophyceae 43
## Cryptophyceae 39
## Dictyochophyceae 43
## Dinophyceae 43
## Eustigmatophyceae 42
## IncertaeSedis_Archaeplastida 1
## Mamiellophyceae 41
## Nephroselmidophyceae 19
## Pavlovophyceae 37
## Pelagophyceae 43
## Phaeophyceae 4
## Phaeothamniophyceae 1
## Prasinophyceae_clade-IX 29
## Prasinophyceae_clade-VII 42
## Prymnesiophyceae 43
## Pyramimonadaceae 33
## Rhodophyceae 13
## Trebouxiophyceae 26
## Ulvophyceae 3
## Xanthophyceae 14
## other_Prasinophyceae 41
Relative values
## reads_per_class OTUs_per_class samples_per_class
## 100.000 100.000 1748.837## reads_per_class OTUs_per_class
## Bacillariophyceae 2.657569e+00 12.97709924
## Bolidophyceae 5.077712e-01 0.86745316
## Chlorarachniophyceae 3.262106e-01 0.69396253
## Chlorophyceae 7.880928e-02 1.56141568
## Chrysophyceae 2.817182e+00 8.32755031
## Cryptophyceae 1.917360e+00 3.29632200
## Dictyochophyceae 2.812194e+00 1.80430257
## Dinophyceae 2.357994e+01 51.21443442
## Eustigmatophyceae 3.581333e-01 0.93684941
## IncertaeSedis_Archaeplastida 9.975858e-04 0.03469813
## Mamiellophyceae 1.580775e+01 4.05968078
## Nephroselmidophyceae 6.384549e-02 0.24288688
## Pavlovophyceae 2.274496e-01 0.45107564
## Pelagophyceae 9.283534e+00 0.86745316
## Phaeophyceae 4.987929e-03 0.13879251
## Phaeothamniophyceae 9.975858e-04 0.03469813
## Prasinophyceae_clade-IX 1.546258e-01 0.55517002
## Prasinophyceae_clade-VII 3.566369e+00 1.28383067
## Prymnesiophyceae 3.467409e+01 6.14156836
## Pyramimonadaceae 5.057760e-01 0.65926440
## Rhodophyceae 1.596137e-02 0.41637752
## Trebouxiophyceae 1.207079e-01 1.97779320
## Ulvophyceae 5.985515e-03 0.17349063
## Xanthophyceae 2.094930e-02 0.38167939
## other_Prasinophyceae 4.908122e-01 0.90215128
## samples_per_class
## Bacillariophyceae 97.674419
## Bolidophyceae 100.000000
## Chlorarachniophyceae 95.348837
## Chlorophyceae 60.465116
## Chrysophyceae 100.000000
## Cryptophyceae 90.697674
## Dictyochophyceae 100.000000
## Dinophyceae 100.000000
## Eustigmatophyceae 97.674419
## IncertaeSedis_Archaeplastida 2.325581
## Mamiellophyceae 95.348837
## Nephroselmidophyceae 44.186047
## Pavlovophyceae 86.046512
## Pelagophyceae 100.000000
## Phaeophyceae 9.302326
## Phaeothamniophyceae 2.325581
## Prasinophyceae_clade-IX 67.441860
## Prasinophyceae_clade-VII 97.674419
## Prymnesiophyceae 100.000000
## Pyramimonadaceae 76.744186
## Rhodophyceae 30.232558
## Trebouxiophyceae 60.465116
## Ulvophyceae 6.976744
## Xanthophyceae 32.558140
## other_Prasinophyceae 95.348837
Reads per class vs. OTUs per class:
Reads per class vs. samples in which they occurr:
2) 16S amplicons
2.1) Data overview
The dataset “Taraspina 16S miTags” contains reads from 45 samples of Tara Oceans and from 10 samples of Malaspina. On average, each sample contains 77920 OTUs:
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 13690 50950 83020 77920 100900 158900
Overall reads per sample:
2.2) Normalization
In order to keep as many samples as possible, we rarefy at 36155 reads per sample. By that, we loose 10 samples, and after removing the exluded samples in the 18S dataset (to make them comparable), we end up with a normalized dataset containing 43 samples and 24691 OTUs.
Datasets summary:
dim(tb16_tax) #original dataset## [1] 28294 58dim(tb16_tax_occur) #original dataset with occurrence data alone## [1] 28294 55dim(tb16_tax_occur_min36155) #dataset without samples with less than 36155 OTUs## [1] 24691 43dim(tb16_tax_occur_ss36155_no_cero) #rarefied dataset## [1] 43 197262.3) General community analysis
2.3.1) Richness and evenness (Shannon index)
Most of the samples take Shannon Index values around 6:
2.3.2) Richness: OTU number
Lowest number of OTUs per sample:
## [1] 2503Maximum number of OTUs per sample:
## [1] 5092In most of the samples, we can identify around 4000 OTUs:
2.3.3) Index of evenness
2.3.3.1) Pielou’s index
The Pielou index (constrained between 0 and 1) takes values closer to 1 as the variation of species proportion in a sample increases. Most of the samples get values around 0.85, meaning that the numerical composition of different OTUs in a sample is highly variable - there’s no constant presence of dominant species.
Most of the OTUs show very few occurrences, suggesting that we will probably be able to identify a significant ammount of rare otus:
2.3.4) Abundance Models
2.3.4.1) Rank-Abundance or Dominance/Diversity Model (“radfit”)
The OTUs abundance distribution fits relativelly close to log-normal model.
2.3.4.2) Preston’s Lognormal Model
According to Preston’s lognormal model fit into species frequencies groups, we’re missing 83761.1 species:
## Extrapolated Observed Veiled
## 108452.1 24691.0 83761.1
When computing Prestons’ lognormal model fit without pooling data into groups, we seem to miss 50576.64 species:
## Extrapolated Observed Veiled
## 75267.64 24691.00 50576.642.3.5) Rarefaction curves of rarefied and non-rarefied datasets
2.3.6) Beta diversity
2.3.6.1) Dissimilarity matrix using Bray-Curtis index:
The Bray-Curtis dissimilarity, constrained between 0 (minimum distance) and 1 (highest dissimilarity) allows us to quantify the differences between samples according to the composition and relative abundance of their OTUs. In our dataset, most of the samples pairs take dissimilarity values around 0.5, meaning that their composition is substantially different.
2.3.6.2) Hierarchical clustering
The stations seem to form clusters according to geographic localization, but there are no evident clusters separated from the general groups, apart from the one containing TARA_84, TARA_82 and TARA_85.
(To be done: assign Longhurst provinces information to each station and check if any of the central clusters is meaningful regarding to the samples’ geographical location)
2.3.6.3) Non-metric multidimensional scaling
We can identify an evident division between the stations close to Southern Ocean (TARA 82, 84 and 85) and the rest of the samples. The stress parameter takes a value below 0.2, suggesting that the plot is acceptable.
##
## Call:
## monoMDS(dist = tb16_tax_occur_ss36155_no_cero.bray)
##
## Non-metric Multidimensional Scaling
##
## 43 points, dissimilarity 'bray', call 'vegdist(x = tb16_tax_occur_ss36155_no_cero, method = "bray")'
##
## Dimensions: 2
## Stress: 9.41416e-05
## Stress type 1, weak ties
## Scores scaled to unit root mean square, rotated to principal components
## Stopped after 69 iterations: Stress nearly zero (< smin)
When implementing a most robut function for computing NMDS plots, the result is quiet the same:
2.4) Geographical analysis
Communities quickly change their composition across geographical distances:
2.4.1) Mantel correlograms
Mantel statistic is -significantlly- so low, meaning that the correlation between samples dissimilarity and geographical distances is weak.
##
## Mantel statistic based on Pearson's product-moment correlation
##
## Call:
## mantel(xdis = geo_distances_MP_16S, ydis = tb16_tax_occur_ss36155_no_cero.bray)
##
## Mantel statistic r: 0.02882
## Significance: 0.278
##
## Upper quantiles of permutations (null model):
## 90% 95% 97.5% 99%
## 0.0794 0.1105 0.1462 0.1687
## Permutation: free
## Number of permutations: 999Correlograms:
MP_16s_ss36155_mantel_correl_by_1000km<-mantel.correlog(tb16_tax_occur_ss36155_no_cero.bray, D.geo=geo_distances_MP_16S, break.pts=seq(0,20000, by=1000))
plot(MP_16s_ss36155_mantel_correl_by_1000km)
MP_16s_ss36155_mantel_correl_by_100km<-mantel.correlog(tb16_tax_occur_ss36155_no_cero.bray, D.geo=geo_distances_MP_16S, break.pts=seq(0,20000, by=100))
plot(MP_16s_ss36155_mantel_correl_by_100km)
2.5) Abundance vs. occurence
OTUs distribution according to their percentage of occurence and relative abundance.
- red line: OTUs that occur in more than 80% of the samples.
- blue line: regionally abundant OTUs (> 0.1%).
- green line: regionally rare OTUs (< 0.001%).
Regionally abundant OTUs (relative abundance over 0.1%):
## otu_names mean_rabund perc_occur class_B
## 6 OTU_1754 0.011012662 93.02326 Prochlorococcus
## 25 OTU_2893 0.008765876 93.02326 other_bacteria
## 135 OTU_761 0.008455198 93.02326 Prochlorococcus
## 10 OTU_2428 0.007725137 93.02326 other_bacteria
## 46 OTU_3736 0.007143661 90.69767 Prochlorococcus
## 7 OTU_1942 0.006589201 93.02326 Prochlorococcus
## 11 OTU_2466 0.006459913 93.02326 Prochlorococcus
## 38 OTU_3271 0.005548462 90.69767 Prochlorococcus
## 69 OTU_5398 0.005484140 90.69767 Prochlorococcus
## 66 OTU_5330 0.004975992 93.02326 Prochlorococcus
## 16 OTU_27927 0.003864498 48.83721 Mamiellophyceae
## 67 OTU_5352 0.003861282 55.81395 other_bacteria
## 32 OTU_3187 0.003603992 100.00000 other_bacteria
## 14 OTU_27901 0.003573760 86.04651 Prymnesiophyceae
## 23 OTU_2866 0.003493357 93.02326 other_bacteria
## 125 OTU_6083 0.003113211 86.04651 Synechococcus
## 137 OTU_8011 0.003112568 86.04651 other_bacteria
## 130 OTU_635 0.003076547 93.02326 other_bacteria
## 131 OTU_709 0.002999360 93.02326 other_bacteria
## 30 OTU_3172 0.002929892 86.04651 other_bacteria
## 40 OTU_3311 0.002813468 93.02326 Prochlorococcus
## 99 OTU_5727 0.002681607 93.02326 other_bacteria
## 37 OTU_3259 0.002622430 60.46512 other_bacteria
## 26 OTU_29 0.002468056 100.00000 other_bacteria
## 77 OTU_5447 0.002439111 100.00000 other_bacteria
## 13 OTU_27900 0.002411452 100.00000 Prymnesiophyceae
## 29 OTU_3162 0.002374788 95.34884 other_bacteria
## 51 OTU_4048 0.002309822 100.00000 other_bacteria
## 70 OTU_5403 0.002296315 90.69767 other_bacteria
## 74 OTU_5432 0.002243570 93.02326 other_bacteria
## 90 OTU_5633 0.002224917 95.34884 other_bacteria
## 3 OTU_1329 0.002220414 93.02326 other_bacteria
## 75 OTU_5441 0.002144513 95.34884 other_bacteria
## 22 OTU_28061 0.002136152 53.48837 Mamiellophyceae
## 27 OTU_3004 0.002114282 93.02326 other_bacteria
## 128 OTU_6164 0.002097558 93.02326 other_bacteria
## 24 OTU_2877 0.002078261 95.34884 other_bacteria
## 140 OTU_8163 0.002048030 100.00000 other_bacteria
## 39 OTU_3308 0.002037095 97.67442 Synechococcus
## 116 OTU_5961 0.002023587 100.00000 other_bacteria
## 4 OTU_1676 0.002010079 88.37209 Prochlorococcus
## 91 OTU_5635 0.002004290 100.00000 other_bacteria
## 5 OTU_1738 0.001992712 93.02326 other_bacteria
## 119 OTU_5978 0.001988853 100.00000 other_bacteria
## 28 OTU_3023 0.001945757 93.02326 other_bacteria
## 139 OTU_8153 0.001932249 93.02326 other_bacteria
## 124 OTU_6067 0.001862138 100.00000 other_bacteria
## 103 OTU_5772 0.001851203 100.00000 other_bacteria
## 102 OTU_5752 0.001832549 93.02326 Prochlorococcus
## 15 OTU_27912 0.001810036 37.20930 Prymnesiophyceae
## 33 OTU_3197 0.001805534 83.72093 other_bacteria
## 64 OTU_5301 0.001798458 95.34884 other_bacteria
## 49 OTU_3810 0.001779161 90.69767 other_bacteria
## 93 OTU_5653 0.001776589 93.02326 other_bacteria
## 36 OTU_3240 0.001768227 93.02326 other_bacteria
## 54 OTU_4560 0.001750216 100.00000 other_bacteria
## 55 OTU_4664 0.001741854 100.00000 other_bacteria
## 53 OTU_4366 0.001713552 100.00000 other_bacteria
## 111 OTU_5879 0.001704547 93.02326 other_bacteria
## 56 OTU_4926 0.001692326 95.34884 other_bacteria
## 44 OTU_3680 0.001641511 100.00000 other_bacteria
## 17 OTU_27934 0.001637009 95.34884 Prymnesiophyceae
## 42 OTU_333 0.001620285 100.00000 other_bacteria
## 145 OTU_9255 0.001613209 83.72093 Synechococcus
## 65 OTU_5327 0.001557892 93.02326 other_bacteria
## 57 OTU_4991 0.001542454 97.67442 other_bacteria
## 72 OTU_542 0.001507720 93.02326 other_bacteria
## 127 OTU_6155 0.001501288 100.00000 other_bacteria
## 88 OTU_5607 0.001487137 93.02326 other_bacteria
## 136 OTU_7987 0.001462051 100.00000 other_bacteria
## 45 OTU_3731 0.001457549 97.67442 other_bacteria
## 9 OTU_23 0.001426674 93.02326 other_bacteria
## 98 OTU_5691 0.001422815 93.02326 other_bacteria
## 34 OTU_3198 0.001422171 97.67442 other_bacteria
## 121 OTU_5985 0.001413166 100.00000 other_bacteria
## 106 OTU_5804 0.001411880 93.02326 other_bacteria
## 94 OTU_5662 0.001399015 90.69767 other_bacteria
## 18 OTU_27938 0.001382291 90.69767 Pelagophyceae
## 117 OTU_5968 0.001375859 100.00000 other_bacteria
## 141 OTU_8367 0.001374573 100.00000 other_bacteria
## 95 OTU_5665 0.001373929 93.02326 other_bacteria
## 100 OTU_5741 0.001367497 100.00000 other_bacteria
## 92 OTU_5651 0.001365568 93.02326 other_bacteria
## 50 OTU_4036 0.001363638 97.67442 other_bacteria
## 48 OTU_3803 0.001359135 100.00000 other_bacteria
## 114 OTU_5925 0.001358492 88.37209 other_bacteria
## 96 OTU_5667 0.001355919 93.02326 other_bacteria
## 82 OTU_5500 0.001351417 100.00000 other_bacteria
## 101 OTU_5742 0.001345628 93.02326 other_bacteria
## 86 OTU_5564 0.001339838 93.02326 other_bacteria
## 132 OTU_7407 0.001337909 90.69767 other_bacteria
## 113 OTU_5911 0.001327617 100.00000 other_bacteria
## 115 OTU_5942 0.001323758 100.00000 other_bacteria
## 144 OTU_8458 0.001319898 100.00000 other_bacteria
## 126 OTU_6102 0.001308320 93.02326 other_bacteria
## 43 OTU_3347 0.001303175 97.67442 other_bacteria
## 41 OTU_3326 0.001297386 93.02326 other_bacteria
## 110 OTU_5823 0.001294813 93.02326 other_bacteria
## 79 OTU_5491 0.001278089 100.00000 other_bacteria
## 89 OTU_5624 0.001275516 95.34884 other_bacteria
## 83 OTU_5511 0.001268440 93.02326 other_bacteria
## 80 OTU_5493 0.001247214 95.34884 other_bacteria
## 62 OTU_5268 0.001246571 100.00000 other_bacteria
## 76 OTU_5445 0.001245928 100.00000 other_bacteria
## 84 OTU_5519 0.001242711 53.48837 other_bacteria
## 20 OTU_28046 0.001227274 51.16279 Mamiellophyceae
## 61 OTU_5266 0.001225988 93.02326 other_bacteria
## 19 OTU_28017 0.001220842 76.74419 Pelagophyceae
## 87 OTU_5586 0.001216982 95.34884 other_bacteria
## 35 OTU_3214 0.001211193 93.02326 other_bacteria
## 85 OTU_5523 0.001203475 100.00000 other_bacteria
## 104 OTU_5786 0.001200259 86.04651 Synechococcus
## 138 OTU_8146 0.001189324 100.00000 other_bacteria
## 112 OTU_5880 0.001187394 93.02326 other_bacteria
## 78 OTU_5449 0.001184821 93.02326 other_bacteria
## 71 OTU_5414 0.001180962 97.67442 other_bacteria
## 129 OTU_6193 0.001177746 100.00000 other_bacteria
## 142 OTU_8377 0.001172600 100.00000 other_bacteria
## 68 OTU_5355 0.001166811 100.00000 other_bacteria
## 63 OTU_5288 0.001166811 88.37209 Prochlorococcus
## 133 OTU_7455 0.001155233 100.00000 other_bacteria
## 118 OTU_5976 0.001137866 95.34884 other_bacteria
## 146 OTU_9267 0.001118569 83.72093 Synechococcus
## 109 OTU_5821 0.001115996 93.02326 other_bacteria
## 147 OTU_934 0.001105704 100.00000 other_bacteria
## 120 OTU_5982 0.001101845 93.02326 other_bacteria
## 60 OTU_5222 0.001100559 88.37209 other_bacteria
## 123 OTU_6047 0.001096056 100.00000 other_bacteria
## 2 OTU_12129 0.001079975 55.81395 Synechococcus
## 1 OTU_10747 0.001077403 58.13953 other_bacteria
## 143 OTU_8436 0.001076116 100.00000 other_bacteria
## 47 OTU_3789 0.001072257 100.00000 other_bacteria
## 81 OTU_5499 0.001065181 93.02326 other_bacteria
## 59 OTU_5211 0.001064538 97.67442 other_bacteria
## 73 OTU_5428 0.001061322 100.00000 other_bacteria
## 52 OTU_4083 0.001056176 95.34884 other_bacteria
## 134 OTU_759 0.001045241 83.72093 Synechococcus
## 58 OTU_520 0.001040095 93.02326 other_bacteria
## 12 OTU_2789 0.001038809 97.67442 other_bacteria
## 122 OTU_5988 0.001034950 93.02326 other_bacteria
## 97 OTU_5679 0.001029161 93.02326 other_bacteria
## 108 OTU_5817 0.001028517 97.67442 other_bacteria
## 31 OTU_3173 0.001018869 76.74419 other_bacteria
## 21 OTU_28060 0.001018869 41.86047 Mamiellophyceae
## 105 OTU_5800 0.001017583 93.02326 other_bacteria
## 107 OTU_5815 0.001009221 100.00000 other_bacteria
## 8 OTU_223 0.001009221 90.69767 other_bacteria
## OTUId
## 6 CyanoDB_EU802275.1.1357_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 25 SILVA.v123_EU803059.1.1291_Bacteria;Proteobacteria;Gammaproteobacteria;Cellvibrionales;Halieaceae;OM60_NOR5__clade;uncultured_bacterium
## 135 CyanoDB_EU237319.1.1311_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 10 SILVA.v123_EU802338.1.1516_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 46 CyanoDB_EU802420.1.1442_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 7 CyanoDB_EU802966.1.1361_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 11 CyanoDB_EU802290.1.1454_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 38 CyanoDB_AY664090.1.1205_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_Prochlorococcus
## 69 CyanoDB_X52169.1.1473_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 66 CyanoDB_JX945341.1.1455_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 16 PhytoREF_3777_AACY020416011_Eukaryota_Archaeplastida_Chlorophyta_Mamiellophyceae_Mamiellophyceae_X_Mamiellales_Mamiellales_X_Bathycoccaceae_Ostreococcus_Ostreococcus
## 67 SILVA.v123_AACY020549891.3846.5359_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;marine_metagenome
## 32 SILVA.v123_EU802563.1.1450_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 14 PhytoREF_3719_KC900889_Eukaryota_Hacrobia_Haptophyta_Prymnesiophyceae_Prymnesiophyceae_X_Phaeocystales_Phaeocystales_X_Phaeocystaceae_Phaeocystis_Phaeocystis
## 23 SILVA.v123_EF572179.1.1472_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 125 CyanoDB_GU119298.1.1407_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacterium
## 137 SILVA.v123_DQ906760.1.1497_Bacteria;Proteobacteria;Gammaproteobacteria;Arenicellales;Arenicellaceae;Arenicella;uncultured_Antarctic_sea_ice_bacterium
## 130 SILVA.v123_EF573150.1.1450_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 131 SILVA.v123_GU940917.1.1359_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 30 SILVA.v123_AACY020481938.3418.4929_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;marine_metagenome
## 40 CyanoDB_EU804864.1.1440_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 99 SILVA.v123_EU802915.1.1434_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;uncultured_bacterium
## 37 SILVA.v123_DQ009141.1.1996_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_marine_bacterium
## 26 SILVA.v123_EU802811.1.1440_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 77 SILVA.v123_EU804325.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 13 PhytoREF_4979_AB199885_Eukaryota_Hacrobia_Haptophyta_Prymnesiophyceae_Prymnesiophyceae_X_Prymnesiales_Prymnesiales_X_Chrysochromulinaceae_Chrysochromulina_Chrysochromulina
## 29 SILVA.v123_FJ825908.1.1508_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_marine_bacterium
## 51 SILVA.v123_EF572460.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 70 SILVA.v123_EU802502.1.1451_Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;SAR116_clade;uncultured_bacterium
## 74 SILVA.v123_EF574089.1.1525_Bacteria;Marinimicrobia__SAR406_clade_;uncultured_bacterium
## 90 SILVA.v123_FN433431.1.1496_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS5_marine_group;uncultured_Flavobacteriia_bacterium
## 3 SILVA.v123_EU803046.1.1424_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;uncultured;uncultured_bacterium
## 75 SILVA.v123_AACY024102418.157.1623_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;marine_metagenome
## 22 PhytoREF_3323_FN563098_Eukaryota_Archaeplastida_Chlorophyta_Mamiellophyceae_Mamiellophyceae_X_Mamiellales_Mamiellales_X_Mamiellaceae_Micromonas_Micromonas
## 27 SILVA.v123_EF574411.1.1527_Bacteria;Marinimicrobia__SAR406_clade_;uncultured_bacterium
## 128 SILVA.v123_EF572431.1.1517_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 24 SILVA.v123_EU394547.1.1451_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_alpha_proteobacterium
## 140 SILVA.v123_EU050769.1.1397_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_alpha_proteobacterium
## 39 CyanoDB_HQ672155.1.1438_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacterium
## 116 SILVA.v123_JX016743.1.1433_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 4 CyanoDB_EU802429.1.1451_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 91 SILVA.v123_EU800179.1.1374_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 5 SILVA.v123_EU802529.1.1481_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_bacterium
## 119 SILVA.v123_EU802612.1.1434_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_2;uncultured_bacterium
## 28 SILVA.v123_AACY023939069.20.1514_Bacteria;Proteobacteria;Deltaproteobacteria;SAR324_clade_Marine_group_B_;marine_metagenome
## 139 SILVA.v123_AACY020396101.1882.3388_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;marine_metagenome
## 124 SILVA.v123_EU802929.1.1358_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;uncultured_bacterium
## 103 SILVA.v123_EF574626.1.1492_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS4_marine_group;uncultured_bacterium
## 102 CyanoDB_AE017126.353331.354795_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_Prochlorococcus_Prochlorococcus_marinus
## 15 PhytoREF_5417_AB847985_Eukaryota_Hacrobia_Haptophyta_Prymnesiophyceae_Prymnesiophyceae_X_Prymnesiophyceae_XX_Prymnesiophyceae_XXX_Braarudosphaeraceae_Braarudosphaera_Braarudosphaera
## 33 SILVA.v123_AACY020443682.520.1932_Bacteria;Proteobacteria;Alphaproteobacteria;OCS116_clade;marine_metagenome
## 64 SILVA.v123_EF575083.1.1498_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 49 SILVA.v123_EF575067.1.1452_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;uncultured;uncultured_bacterium
## 93 SILVA.v123_EU805216.1.1503_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 36 SILVA.v123_GU940823.1.1357_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_bacterium
## 54 SILVA.v123_EF573299.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 55 SILVA.v123_GU061507.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 53 SILVA.v123_FR684404.1.1435_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_marine_bacterium
## 111 SILVA.v123_EF574657.1.1483_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS4_marine_group;uncultured_bacterium
## 56 SILVA.v123_EU802923.1.1453_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_4;uncultured_bacterium
## 44 SILVA.v123_GQ351167.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 17 PhytoREF_155_Eukaryota_Hacrobia_Haptophyta_Prymnesiophyceae_Prymnesiophyceae_X_Phaeocystales_Phaeocystales_X_Phaeocystaceae_Phaeocystis_Phaeocystis
## 42 SILVA.v123_AF382134.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 145 CyanoDB_AY664003.1.1207_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_Synechococcus
## 65 SILVA.v123_EU802682.1.1495_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 57 SILVA.v123_EU803186.1.1437_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;uncultured;uncultured_bacterium
## 72 SILVA.v123_EF575137.1.1492_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS4_marine_group;uncultured_bacterium
## 127 SILVA.v123_HQ671926.1.1435_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_2;uncultured_bacterium
## 88 SILVA.v123_AY033296.1.1499_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_actinobacterium_MB11A03
## 136 SILVA.v123_EU803121.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 45 SILVA.v123_HQ242370.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_2;uncultured_SAR11_cluster_alpha_proteobacterium
## 9 SILVA.v123_JQ611213.1.1323_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 98 SILVA.v123_JQ516699.1.1498_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_actinobacterium
## 34 SILVA.v123_EU802480.1.1262_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;uncultured_bacterium
## 121 SILVA.v123_AY700640.1.1494_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 106 SILVA.v123_DQ009111.1.2063_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS2b_marine_group;uncultured_marine_bacterium
## 94 SILVA.v123_EF575061.1.1479_Bacteria;Bacteroidetes;Cytophagia;Cytophagales;Flammeovirgaceae;Marinoscillum;uncultured_bacterium
## 18 PhytoREF_2512_NC_012898_Eukaryota_Stramenopiles_Ochrophyta_Pelagophyceae_Pelagophyceae_X_Pelagomonadales_Pelagomonadales_X_Pelagomonadaceae_Aureococcus_Aureococcus
## 117 SILVA.v123_JN976625.1.1411_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 141 SILVA.v123_KF799972.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 95 SILVA.v123_JN985907.1.1452_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_4;uncultured_bacterium
## 100 SILVA.v123_FR683897.1.1434_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_marine_bacterium
## 92 SILVA.v123_JQ516679.1.1511_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_bacterium
## 50 SILVA.v123_EU802672.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 48 SILVA.v123_EU800456.1.1443_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 114 SILVA.v123_EF572710.1.1498_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 96 SILVA.v123_KC872791.1.1339_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 82 SILVA.v123_EU801782.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 101 SILVA.v123_EF572670.1.1440_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_4;uncultured_bacterium
## 86 SILVA.v123_EU802819.1.1500_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 132 SILVA.v123_EF572465.1.1526_Bacteria;Marinimicrobia__SAR406_clade_;uncultured_bacterium
## 113 SILVA.v123_EU805108.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 115 SILVA.v123_EU805259.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 144 SILVA.v123_FR686262.1.1435_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;Candidatus_Pelagibacter;uncultured_marine_bacterium
## 126 SILVA.v123_AF406543.1.1404_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_Gram_positive_bacterium
## 43 SILVA.v123_EU803155.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_2;uncultured_bacterium
## 41 SILVA.v123_EU802374.1.1489_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;uncultured_bacterium
## 110 SILVA.v123_EU803095.1.1260_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 79 SILVA.v123_EU804185.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 89 SILVA.v123_KC872373.1.1325_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 83 SILVA.v123_AACY020563509.792.2305_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;marine_metagenome
## 80 SILVA.v123_KC873625.1.1348_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_2;uncultured_bacterium
## 62 SILVA.v123_AACY023928123.190.1644_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;marine_metagenome
## 76 SILVA.v123_EF574603.1.1499_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 84 SILVA.v123_EF573190.1.1498_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 20 PhytoREF_4604_FN563099_Eukaryota_Archaeplastida_Chlorophyta_Mamiellophyceae_Mamiellophyceae_X_Mamiellales_Mamiellales_X_Bathycoccaceae_Bathycoccus_Bathycoccus
## 61 SILVA.v123_EF572435.1.1502_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS5_marine_group;uncultured_bacterium
## 19 PhytoREF_395_Eukaryota_Stramenopiles_Ochrophyta_Pelagophyceae_Pelagophyceae_X_Pelagomonadales_Pelagomonadales_X_Pelagomonadaceae_Pelagomonas_Pelagomonas
## 87 SILVA.v123_EU802302.1.1503_Bacteria;Proteobacteria;Deltaproteobacteria;SAR324_clade_Marine_group_B_;uncultured_bacterium
## 35 SILVA.v123_JX945338.1.1456_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 85 SILVA.v123_FR684943.1.1434_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_marine_bacterium
## 104 CyanoDB_X52171.1.1477_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacterium
## 138 SILVA.v123_EU259796.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;Candidatus_Pelagibacter;uncultured_bacterium
## 112 SILVA.v123_EU802956.1.1452_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 78 SILVA.v123_EU801696.1.1459_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 71 SILVA.v123_EU802363.1.1438_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 129 SILVA.v123_JN233419.1.1394_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_marine_bacterium
## 142 SILVA.v123_FR686065.1.1435_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_marine_bacterium
## 68 SILVA.v123_EU804555.1.1438_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;Candidatus_Pelagibacter;uncultured_bacterium
## 63 CyanoDB_EU802498.1.1435_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 133 SILVA.v123_EU801950.1.1450_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;Candidatus_Pelagibacter;uncultured_bacterium
## 118 SILVA.v123_AACY020555729.127.1634_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS4_marine_group;marine_metagenome
## 146 CyanoDB_AJ639901.1.1481_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_Aphanothece_Aphanothece_sp.
## 109 SILVA.v123_KC873462.1.1334_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 147 SILVA.v123_FR684827.1.1435_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_marine_bacterium
## 120 SILVA.v123_JQ515581.1.1452_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_alpha_proteobacterium
## 60 SILVA.v123_DQ009261.1.1979_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_marine_bacterium
## 123 SILVA.v123_AY907723.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 2 CyanoDB_JQ062633.1.1427_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacterium
## 1 SILVA.v123_AACY020565564.130.1652_Bacteria;Proteobacteria;Gammaproteobacteria;Salinisphaerales;Salinisphaeraceae;ZD0417_marine_group;marine_metagenome
## 143 SILVA.v123_FJ744886.1.1319_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_2;uncultured_bacterium
## 47 SILVA.v123_EU803119.1.1440_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 81 SILVA.v123_EF573001.1.1489_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Sufflavibacter;uncultured_bacterium
## 59 SILVA.v123_JN986566.1.1485_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS2b_marine_group;uncultured_bacterium
## 73 SILVA.v123_GU940923.1.1380_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 52 SILVA.v123_FN433299.1.1479_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS2b_marine_group;uncultured_Flavobacteriia_bacterium
## 134 CyanoDB_HQ672048.1.1451_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacterium
## 58 SILVA.v123_KC294916.1.1411_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 12 SILVA.v123_EU802269.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 122 SILVA.v123_KC294834.1.1413_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_4;uncultured_bacterium
## 97 SILVA.v123_EU802614.1.1337_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_bacterium
## 108 SILVA.v123_EU805301.1.1438_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_2;uncultured_bacterium
## 31 SILVA.v123_GU235015.1.1323_Bacteria;Lentisphaerae;Lentisphaeria;Lentisphaerales;Lentisphaeraceae;Lentisphaera;uncultured_marine_bacterium
## 21 PhytoREF_765_Eukaryota_Archaeplastida_Chlorophyta_Mamiellophyceae_Mamiellophyceae_X_Mamiellales_Mamiellales_X_Mamiellaceae_Micromonas_Micromonas
## 105 SILVA.v123_EU237342.1.1352_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_bacterium
## 107 SILVA.v123_FR685223.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_marine_bacterium
## 8 SILVA.v123_EF574498.1.1440_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;uncultured;uncultured_bacteriumNumber and roportion of regionally abundant OTUs (%):
## [1] 147## [1] 0.7452094Cosmopolitan OTUs (relative abundance over 0.1% and occurence in more than 80% of samples):
## otu_names mean_rabund perc_occur class_B
## 23 OTU_3187 0.003603992 100.00000 other_bacteria
## 18 OTU_29 0.002468056 100.00000 other_bacteria
## 66 OTU_5447 0.002439111 100.00000 other_bacteria
## 11 OTU_27900 0.002411452 100.00000 Prymnesiophyceae
## 41 OTU_4048 0.002309822 100.00000 other_bacteria
## 128 OTU_8163 0.002048030 100.00000 other_bacteria
## 104 OTU_5961 0.002023587 100.00000 other_bacteria
## 79 OTU_5635 0.002004290 100.00000 other_bacteria
## 107 OTU_5978 0.001988853 100.00000 other_bacteria
## 112 OTU_6067 0.001862138 100.00000 other_bacteria
## 91 OTU_5772 0.001851203 100.00000 other_bacteria
## 44 OTU_4560 0.001750216 100.00000 other_bacteria
## 45 OTU_4664 0.001741854 100.00000 other_bacteria
## 43 OTU_4366 0.001713552 100.00000 other_bacteria
## 34 OTU_3680 0.001641511 100.00000 other_bacteria
## 32 OTU_333 0.001620285 100.00000 other_bacteria
## 115 OTU_6155 0.001501288 100.00000 other_bacteria
## 124 OTU_7987 0.001462051 100.00000 other_bacteria
## 109 OTU_5985 0.001413166 100.00000 other_bacteria
## 105 OTU_5968 0.001375859 100.00000 other_bacteria
## 129 OTU_8367 0.001374573 100.00000 other_bacteria
## 88 OTU_5741 0.001367497 100.00000 other_bacteria
## 38 OTU_3803 0.001359135 100.00000 other_bacteria
## 71 OTU_5500 0.001351417 100.00000 other_bacteria
## 101 OTU_5911 0.001327617 100.00000 other_bacteria
## 103 OTU_5942 0.001323758 100.00000 other_bacteria
## 132 OTU_8458 0.001319898 100.00000 other_bacteria
## 68 OTU_5491 0.001278089 100.00000 other_bacteria
## 52 OTU_5268 0.001246571 100.00000 other_bacteria
## 65 OTU_5445 0.001245928 100.00000 other_bacteria
## 73 OTU_5523 0.001203475 100.00000 other_bacteria
## 126 OTU_8146 0.001189324 100.00000 other_bacteria
## 117 OTU_6193 0.001177746 100.00000 other_bacteria
## 130 OTU_8377 0.001172600 100.00000 other_bacteria
## 57 OTU_5355 0.001166811 100.00000 other_bacteria
## 121 OTU_7455 0.001155233 100.00000 other_bacteria
## 135 OTU_934 0.001105704 100.00000 other_bacteria
## 111 OTU_6047 0.001096056 100.00000 other_bacteria
## 131 OTU_8436 0.001076116 100.00000 other_bacteria
## 37 OTU_3789 0.001072257 100.00000 other_bacteria
## 62 OTU_5428 0.001061322 100.00000 other_bacteria
## 95 OTU_5815 0.001009221 100.00000 other_bacteria
## 29 OTU_3308 0.002037095 97.67442 Synechococcus
## 47 OTU_4991 0.001542454 97.67442 other_bacteria
## 35 OTU_3731 0.001457549 97.67442 other_bacteria
## 25 OTU_3198 0.001422171 97.67442 other_bacteria
## 40 OTU_4036 0.001363638 97.67442 other_bacteria
## 33 OTU_3347 0.001303175 97.67442 other_bacteria
## 60 OTU_5414 0.001180962 97.67442 other_bacteria
## 49 OTU_5211 0.001064538 97.67442 other_bacteria
## 10 OTU_2789 0.001038809 97.67442 other_bacteria
## 96 OTU_5817 0.001028517 97.67442 other_bacteria
## 21 OTU_3162 0.002374788 95.34884 other_bacteria
## 78 OTU_5633 0.002224917 95.34884 other_bacteria
## 64 OTU_5441 0.002144513 95.34884 other_bacteria
## 16 OTU_2877 0.002078261 95.34884 other_bacteria
## 54 OTU_5301 0.001798458 95.34884 other_bacteria
## 46 OTU_4926 0.001692326 95.34884 other_bacteria
## 13 OTU_27934 0.001637009 95.34884 Prymnesiophyceae
## 77 OTU_5624 0.001275516 95.34884 other_bacteria
## 69 OTU_5493 0.001247214 95.34884 other_bacteria
## 75 OTU_5586 0.001216982 95.34884 other_bacteria
## 106 OTU_5976 0.001137866 95.34884 other_bacteria
## 42 OTU_4083 0.001056176 95.34884 other_bacteria
## 4 OTU_1754 0.011012662 93.02326 Prochlorococcus
## 17 OTU_2893 0.008765876 93.02326 other_bacteria
## 123 OTU_761 0.008455198 93.02326 Prochlorococcus
## 8 OTU_2428 0.007725137 93.02326 other_bacteria
## 5 OTU_1942 0.006589201 93.02326 Prochlorococcus
## 9 OTU_2466 0.006459913 93.02326 Prochlorococcus
## 56 OTU_5330 0.004975992 93.02326 Prochlorococcus
## 15 OTU_2866 0.003493357 93.02326 other_bacteria
## 118 OTU_635 0.003076547 93.02326 other_bacteria
## 119 OTU_709 0.002999360 93.02326 other_bacteria
## 30 OTU_3311 0.002813468 93.02326 Prochlorococcus
## 87 OTU_5727 0.002681607 93.02326 other_bacteria
## 63 OTU_5432 0.002243570 93.02326 other_bacteria
## 1 OTU_1329 0.002220414 93.02326 other_bacteria
## 19 OTU_3004 0.002114282 93.02326 other_bacteria
## 116 OTU_6164 0.002097558 93.02326 other_bacteria
## 3 OTU_1738 0.001992712 93.02326 other_bacteria
## 20 OTU_3023 0.001945757 93.02326 other_bacteria
## 127 OTU_8153 0.001932249 93.02326 other_bacteria
## 90 OTU_5752 0.001832549 93.02326 Prochlorococcus
## 81 OTU_5653 0.001776589 93.02326 other_bacteria
## 27 OTU_3240 0.001768227 93.02326 other_bacteria
## 99 OTU_5879 0.001704547 93.02326 other_bacteria
## 55 OTU_5327 0.001557892 93.02326 other_bacteria
## 61 OTU_542 0.001507720 93.02326 other_bacteria
## 76 OTU_5607 0.001487137 93.02326 other_bacteria
## 7 OTU_23 0.001426674 93.02326 other_bacteria
## 86 OTU_5691 0.001422815 93.02326 other_bacteria
## 94 OTU_5804 0.001411880 93.02326 other_bacteria
## 83 OTU_5665 0.001373929 93.02326 other_bacteria
## 80 OTU_5651 0.001365568 93.02326 other_bacteria
## 84 OTU_5667 0.001355919 93.02326 other_bacteria
## 89 OTU_5742 0.001345628 93.02326 other_bacteria
## 74 OTU_5564 0.001339838 93.02326 other_bacteria
## 114 OTU_6102 0.001308320 93.02326 other_bacteria
## 31 OTU_3326 0.001297386 93.02326 other_bacteria
## 98 OTU_5823 0.001294813 93.02326 other_bacteria
## 72 OTU_5511 0.001268440 93.02326 other_bacteria
## 51 OTU_5266 0.001225988 93.02326 other_bacteria
## 26 OTU_3214 0.001211193 93.02326 other_bacteria
## 100 OTU_5880 0.001187394 93.02326 other_bacteria
## 67 OTU_5449 0.001184821 93.02326 other_bacteria
## 97 OTU_5821 0.001115996 93.02326 other_bacteria
## 108 OTU_5982 0.001101845 93.02326 other_bacteria
## 70 OTU_5499 0.001065181 93.02326 other_bacteria
## 48 OTU_520 0.001040095 93.02326 other_bacteria
## 110 OTU_5988 0.001034950 93.02326 other_bacteria
## 85 OTU_5679 0.001029161 93.02326 other_bacteria
## 93 OTU_5800 0.001017583 93.02326 other_bacteria
## 36 OTU_3736 0.007143661 90.69767 Prochlorococcus
## 28 OTU_3271 0.005548462 90.69767 Prochlorococcus
## 58 OTU_5398 0.005484140 90.69767 Prochlorococcus
## 59 OTU_5403 0.002296315 90.69767 other_bacteria
## 39 OTU_3810 0.001779161 90.69767 other_bacteria
## 82 OTU_5662 0.001399015 90.69767 other_bacteria
## 14 OTU_27938 0.001382291 90.69767 Pelagophyceae
## 120 OTU_7407 0.001337909 90.69767 other_bacteria
## 6 OTU_223 0.001009221 90.69767 other_bacteria
## 2 OTU_1676 0.002010079 88.37209 Prochlorococcus
## 102 OTU_5925 0.001358492 88.37209 other_bacteria
## 53 OTU_5288 0.001166811 88.37209 Prochlorococcus
## 50 OTU_5222 0.001100559 88.37209 other_bacteria
## 12 OTU_27901 0.003573760 86.04651 Prymnesiophyceae
## 113 OTU_6083 0.003113211 86.04651 Synechococcus
## 125 OTU_8011 0.003112568 86.04651 other_bacteria
## 22 OTU_3172 0.002929892 86.04651 other_bacteria
## 92 OTU_5786 0.001200259 86.04651 Synechococcus
## 24 OTU_3197 0.001805534 83.72093 other_bacteria
## 133 OTU_9255 0.001613209 83.72093 Synechococcus
## 134 OTU_9267 0.001118569 83.72093 Synechococcus
## 122 OTU_759 0.001045241 83.72093 Synechococcus
## OTUId
## 23 SILVA.v123_EU802563.1.1450_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 18 SILVA.v123_EU802811.1.1440_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 66 SILVA.v123_EU804325.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 11 PhytoREF_4979_AB199885_Eukaryota_Hacrobia_Haptophyta_Prymnesiophyceae_Prymnesiophyceae_X_Prymnesiales_Prymnesiales_X_Chrysochromulinaceae_Chrysochromulina_Chrysochromulina
## 41 SILVA.v123_EF572460.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 128 SILVA.v123_EU050769.1.1397_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_alpha_proteobacterium
## 104 SILVA.v123_JX016743.1.1433_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 79 SILVA.v123_EU800179.1.1374_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 107 SILVA.v123_EU802612.1.1434_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_2;uncultured_bacterium
## 112 SILVA.v123_EU802929.1.1358_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;uncultured_bacterium
## 91 SILVA.v123_EF574626.1.1492_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS4_marine_group;uncultured_bacterium
## 44 SILVA.v123_EF573299.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 45 SILVA.v123_GU061507.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 43 SILVA.v123_FR684404.1.1435_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_marine_bacterium
## 34 SILVA.v123_GQ351167.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 32 SILVA.v123_AF382134.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 115 SILVA.v123_HQ671926.1.1435_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_2;uncultured_bacterium
## 124 SILVA.v123_EU803121.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 109 SILVA.v123_AY700640.1.1494_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 105 SILVA.v123_JN976625.1.1411_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 129 SILVA.v123_KF799972.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 88 SILVA.v123_FR683897.1.1434_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_marine_bacterium
## 38 SILVA.v123_EU800456.1.1443_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 71 SILVA.v123_EU801782.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 101 SILVA.v123_EU805108.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 103 SILVA.v123_EU805259.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 132 SILVA.v123_FR686262.1.1435_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;Candidatus_Pelagibacter;uncultured_marine_bacterium
## 68 SILVA.v123_EU804185.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 52 SILVA.v123_AACY023928123.190.1644_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;marine_metagenome
## 65 SILVA.v123_EF574603.1.1499_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 73 SILVA.v123_FR684943.1.1434_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_marine_bacterium
## 126 SILVA.v123_EU259796.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;Candidatus_Pelagibacter;uncultured_bacterium
## 117 SILVA.v123_JN233419.1.1394_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_marine_bacterium
## 130 SILVA.v123_FR686065.1.1435_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_marine_bacterium
## 57 SILVA.v123_EU804555.1.1438_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;Candidatus_Pelagibacter;uncultured_bacterium
## 121 SILVA.v123_EU801950.1.1450_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;Candidatus_Pelagibacter;uncultured_bacterium
## 135 SILVA.v123_FR684827.1.1435_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_marine_bacterium
## 111 SILVA.v123_AY907723.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 131 SILVA.v123_FJ744886.1.1319_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_2;uncultured_bacterium
## 37 SILVA.v123_EU803119.1.1440_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 62 SILVA.v123_GU940923.1.1380_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 95 SILVA.v123_FR685223.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_marine_bacterium
## 29 CyanoDB_HQ672155.1.1438_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacterium
## 47 SILVA.v123_EU803186.1.1437_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;uncultured;uncultured_bacterium
## 35 SILVA.v123_HQ242370.1.1436_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_2;uncultured_SAR11_cluster_alpha_proteobacterium
## 25 SILVA.v123_EU802480.1.1262_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;uncultured_bacterium
## 40 SILVA.v123_EU802672.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 33 SILVA.v123_EU803155.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_2;uncultured_bacterium
## 60 SILVA.v123_EU802363.1.1438_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 49 SILVA.v123_JN986566.1.1485_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS2b_marine_group;uncultured_bacterium
## 10 SILVA.v123_EU802269.1.1439_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_1;uncultured_bacterium
## 96 SILVA.v123_EU805301.1.1438_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_2;uncultured_bacterium
## 21 SILVA.v123_FJ825908.1.1508_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_marine_bacterium
## 78 SILVA.v123_FN433431.1.1496_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS5_marine_group;uncultured_Flavobacteriia_bacterium
## 64 SILVA.v123_AACY024102418.157.1623_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;marine_metagenome
## 16 SILVA.v123_EU394547.1.1451_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_alpha_proteobacterium
## 54 SILVA.v123_EF575083.1.1498_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 46 SILVA.v123_EU802923.1.1453_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_4;uncultured_bacterium
## 13 PhytoREF_155_Eukaryota_Hacrobia_Haptophyta_Prymnesiophyceae_Prymnesiophyceae_X_Phaeocystales_Phaeocystales_X_Phaeocystaceae_Phaeocystis_Phaeocystis
## 77 SILVA.v123_KC872373.1.1325_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 69 SILVA.v123_KC873625.1.1348_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_2;uncultured_bacterium
## 75 SILVA.v123_EU802302.1.1503_Bacteria;Proteobacteria;Deltaproteobacteria;SAR324_clade_Marine_group_B_;uncultured_bacterium
## 106 SILVA.v123_AACY020555729.127.1634_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS4_marine_group;marine_metagenome
## 42 SILVA.v123_FN433299.1.1479_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS2b_marine_group;uncultured_Flavobacteriia_bacterium
## 4 CyanoDB_EU802275.1.1357_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 17 SILVA.v123_EU803059.1.1291_Bacteria;Proteobacteria;Gammaproteobacteria;Cellvibrionales;Halieaceae;OM60_NOR5__clade;uncultured_bacterium
## 123 CyanoDB_EU237319.1.1311_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 8 SILVA.v123_EU802338.1.1516_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 5 CyanoDB_EU802966.1.1361_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 9 CyanoDB_EU802290.1.1454_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 56 CyanoDB_JX945341.1.1455_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 15 SILVA.v123_EF572179.1.1472_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 118 SILVA.v123_EF573150.1.1450_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 119 SILVA.v123_GU940917.1.1359_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 30 CyanoDB_EU804864.1.1440_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 87 SILVA.v123_EU802915.1.1434_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;uncultured_bacterium
## 63 SILVA.v123_EF574089.1.1525_Bacteria;Marinimicrobia__SAR406_clade_;uncultured_bacterium
## 1 SILVA.v123_EU803046.1.1424_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;uncultured;uncultured_bacterium
## 19 SILVA.v123_EF574411.1.1527_Bacteria;Marinimicrobia__SAR406_clade_;uncultured_bacterium
## 116 SILVA.v123_EF572431.1.1517_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 3 SILVA.v123_EU802529.1.1481_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_bacterium
## 20 SILVA.v123_AACY023939069.20.1514_Bacteria;Proteobacteria;Deltaproteobacteria;SAR324_clade_Marine_group_B_;marine_metagenome
## 127 SILVA.v123_AACY020396101.1882.3388_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;marine_metagenome
## 90 CyanoDB_AE017126.353331.354795_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_Prochlorococcus_Prochlorococcus_marinus
## 81 SILVA.v123_EU805216.1.1503_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 27 SILVA.v123_GU940823.1.1357_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_bacterium
## 99 SILVA.v123_EF574657.1.1483_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS4_marine_group;uncultured_bacterium
## 55 SILVA.v123_EU802682.1.1495_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 61 SILVA.v123_EF575137.1.1492_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS4_marine_group;uncultured_bacterium
## 76 SILVA.v123_AY033296.1.1499_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_actinobacterium_MB11A03
## 7 SILVA.v123_JQ611213.1.1323_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 86 SILVA.v123_JQ516699.1.1498_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_actinobacterium
## 94 SILVA.v123_DQ009111.1.2063_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS2b_marine_group;uncultured_marine_bacterium
## 83 SILVA.v123_JN985907.1.1452_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_4;uncultured_bacterium
## 80 SILVA.v123_JQ516679.1.1511_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_bacterium
## 84 SILVA.v123_KC872791.1.1339_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 89 SILVA.v123_EF572670.1.1440_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_4;uncultured_bacterium
## 74 SILVA.v123_EU802819.1.1500_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 114 SILVA.v123_AF406543.1.1404_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_Gram_positive_bacterium
## 31 SILVA.v123_EU802374.1.1489_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;uncultured_bacterium
## 98 SILVA.v123_EU803095.1.1260_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 72 SILVA.v123_AACY020563509.792.2305_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;marine_metagenome
## 51 SILVA.v123_EF572435.1.1502_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;NS5_marine_group;uncultured_bacterium
## 26 SILVA.v123_JX945338.1.1456_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 100 SILVA.v123_EU802956.1.1452_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 67 SILVA.v123_EU801696.1.1459_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 97 SILVA.v123_KC873462.1.1334_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 108 SILVA.v123_JQ515581.1.1452_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_alpha_proteobacterium
## 70 SILVA.v123_EF573001.1.1489_Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Sufflavibacter;uncultured_bacterium
## 48 SILVA.v123_KC294916.1.1411_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_bacterium
## 110 SILVA.v123_KC294834.1.1413_Bacteria;Proteobacteria;Alphaproteobacteria;SAR11_clade;Surface_4;uncultured_bacterium
## 85 SILVA.v123_EU802614.1.1337_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_bacterium
## 93 SILVA.v123_EU237342.1.1352_Bacteria;Actinobacteria;Acidimicrobiia;Acidimicrobiales;OM1_clade;Candidatus_Actinomarina;uncultured_bacterium
## 36 CyanoDB_EU802420.1.1442_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 28 CyanoDB_AY664090.1.1205_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_Prochlorococcus
## 58 CyanoDB_X52169.1.1473_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 59 SILVA.v123_EU802502.1.1451_Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;SAR116_clade;uncultured_bacterium
## 39 SILVA.v123_EF575067.1.1452_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;uncultured;uncultured_bacterium
## 82 SILVA.v123_EF575061.1.1479_Bacteria;Bacteroidetes;Cytophagia;Cytophagales;Flammeovirgaceae;Marinoscillum;uncultured_bacterium
## 14 PhytoREF_2512_NC_012898_Eukaryota_Stramenopiles_Ochrophyta_Pelagophyceae_Pelagophyceae_X_Pelagomonadales_Pelagomonadales_X_Pelagomonadaceae_Aureococcus_Aureococcus
## 120 SILVA.v123_EF572465.1.1526_Bacteria;Marinimicrobia__SAR406_clade_;uncultured_bacterium
## 6 SILVA.v123_EF574498.1.1440_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;uncultured;uncultured_bacterium
## 2 CyanoDB_EU802429.1.1451_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 102 SILVA.v123_EF572710.1.1498_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;uncultured_bacterium
## 53 CyanoDB_EU802498.1.1435_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 50 SILVA.v123_DQ009261.1.1979_Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;AEGEAN_169_marine_group;uncultured_marine_bacterium
## 12 PhytoREF_3719_KC900889_Eukaryota_Hacrobia_Haptophyta_Prymnesiophyceae_Prymnesiophyceae_X_Phaeocystales_Phaeocystales_X_Phaeocystaceae_Phaeocystis_Phaeocystis
## 113 CyanoDB_GU119298.1.1407_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacterium
## 125 SILVA.v123_DQ906760.1.1497_Bacteria;Proteobacteria;Gammaproteobacteria;Arenicellales;Arenicellaceae;Arenicella;uncultured_Antarctic_sea_ice_bacterium
## 22 SILVA.v123_AACY020481938.3418.4929_Bacteria;Proteobacteria;Gammaproteobacteria;Oceanospirillales;SAR86_clade;marine_metagenome
## 92 CyanoDB_X52171.1.1477_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacterium
## 24 SILVA.v123_AACY020443682.520.1932_Bacteria;Proteobacteria;Alphaproteobacteria;OCS116_clade;marine_metagenome
## 133 CyanoDB_AY664003.1.1207_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_Synechococcus
## 134 CyanoDB_AJ639901.1.1481_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_Aphanothece_Aphanothece_sp.
## 122 CyanoDB_HQ672048.1.1451_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacteriumNumber and proportion (%) of cosmopolitan OTUs:
## [1] 135## [1] 0.684376Number and proportion (%) of rare OTUs:
## [1] 13915## [1] 70.541422.6) Taxonomic composition analysis
2.6.1) Normalized data
No. of OTUs and reads of the rearefied dataset:
## [1] 19726## [1] 1554665No. of OTUs and reads of phototrophic groups:
## [1] 660## [1] 223710No. of OTUs and reads of non-phototrophic groups:
## [1] 19066## [1] 1330955
PHOTOTROPHS + HETEROTROPHS
Absolute values
## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 730 132 36
## Bolidophyceae 173 6 28
## Chlorarachniophyceae 14 4 5
## Chlorodendrophyceae 1 1 1
## Chlorophyceae 1 1 1
## Cryptophyceae 1764 26 28
## Cyanobacteria 171040 346 43
## Dictyochophyceae 1282 7 42
## Dinophyceae 12 5 8
## Eustigmatophyceae 14 2 7
## Mamiellophyceae 15820 14 30
## Pavlovophyceae 2 1 2
## Pelagophyceae 5550 10 43
## Phaeophyceae 2 2 2
## Pinguiophyceae 1 1 1
## Prymnesiophyceae 25887 50 43
## Pyramimonadaceae 76 6 9
## Rappemonads 133 4 29
## Trebouxiophyceae 1 1 1
## other_Prasinophyceae 1154 21 38
## other_bacteria 1330955 19066 43
## other_plastids 53 20 20
Relative values
## reads_per_class OTUs_per_class samples_per_class
## 100.000 100.000 1069.767## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 4.695545e-02 0.669167596 83.720930
## Bolidophyceae 1.112780e-02 0.030416709 65.116279
## Chlorarachniophyceae 9.005155e-04 0.020277806 11.627907
## Chlorodendrophyceae 6.432254e-05 0.005069451 2.325581
## Chlorophyceae 6.432254e-05 0.005069451 2.325581
## Cryptophyceae 1.134650e-01 0.131805739 65.116279
## Cyanobacteria 1.100173e+01 1.754030214 100.000000
## Dictyochophyceae 8.246149e-02 0.035486160 97.674419
## Dinophyceae 7.718705e-04 0.025347257 18.604651
## Eustigmatophyceae 9.005155e-04 0.010138903 16.279070
## Mamiellophyceae 1.017583e+00 0.070972321 69.767442
## Pavlovophyceae 1.286451e-04 0.005069451 4.651163
## Pelagophyceae 3.569901e-01 0.050694515 100.000000
## Phaeophyceae 1.286451e-04 0.010138903 4.651163
## Pinguiophyceae 6.432254e-05 0.005069451 2.325581
## Prymnesiophyceae 1.665118e+00 0.253472574 100.000000
## Pyramimonadaceae 4.888513e-03 0.030416709 20.930233
## Rappemonads 8.554898e-03 0.020277806 67.441860
## Trebouxiophyceae 6.432254e-05 0.005069451 2.325581
## other_Prasinophyceae 7.422821e-02 0.106458481 88.372093
## other_bacteria 8.561040e+01 96.654162020 100.000000
## other_plastids 3.409095e-03 0.101389030 46.511628
Reads per class vs. OTUs per class:
Reads per class vs. samples in which they occurr:
PHOTOTROPHS
Absolute values
## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 730 132 36
## Bolidophyceae 173 6 28
## Chlorarachniophyceae 14 4 5
## Chlorodendrophyceae 1 1 1
## Chlorophyceae 1 1 1
## Cryptophyceae 1764 26 28
## Cyanobacteria 171040 346 43
## Dictyochophyceae 1282 7 42
## Dinophyceae 12 5 8
## Eustigmatophyceae 14 2 7
## Mamiellophyceae 15820 14 30
## Pavlovophyceae 2 1 2
## Pelagophyceae 5550 10 43
## Phaeophyceae 2 2 2
## Pinguiophyceae 1 1 1
## Prymnesiophyceae 25887 50 43
## Pyramimonadaceae 76 6 9
## Rappemonads 133 4 29
## Trebouxiophyceae 1 1 1
## other_Prasinophyceae 1154 21 38
## other_plastids 53 20 20
Relative values
## reads_per_class OTUs_per_class samples_per_class
## 100.0000 100.0000 969.7674## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 3.263153e-01 20.0000000 83.720930
## Bolidophyceae 7.733226e-02 0.9090909 65.116279
## Chlorarachniophyceae 6.258102e-03 0.6060606 11.627907
## Chlorodendrophyceae 4.470073e-04 0.1515152 2.325581
## Chlorophyceae 4.470073e-04 0.1515152 2.325581
## Cryptophyceae 7.885209e-01 3.9393939 65.116279
## Cyanobacteria 7.645613e+01 52.4242424 100.000000
## Dictyochophyceae 5.730633e-01 1.0606061 97.674419
## Dinophyceae 5.364087e-03 0.7575758 18.604651
## Eustigmatophyceae 6.258102e-03 0.3030303 16.279070
## Mamiellophyceae 7.071655e+00 2.1212121 69.767442
## Pavlovophyceae 8.940146e-04 0.1515152 4.651163
## Pelagophyceae 2.480890e+00 1.5151515 100.000000
## Phaeophyceae 8.940146e-04 0.3030303 4.651163
## Pinguiophyceae 4.470073e-04 0.1515152 2.325581
## Prymnesiophyceae 1.157168e+01 7.5757576 100.000000
## Pyramimonadaceae 3.397255e-02 0.9090909 20.930233
## Rappemonads 5.945197e-02 0.6060606 67.441860
## Trebouxiophyceae 4.470073e-04 0.1515152 2.325581
## other_Prasinophyceae 5.158464e-01 3.1818182 88.372093
## other_plastids 2.369139e-02 3.0303030 46.511628
Reads per class vs. OTUs per class:
Reads per class vs. samples in which they occurr:
2.6.2) Non-rarefied data
Let’s add the taxonomic classification by merging “tb16_tax_occur_min36155_t” with “tb16_tax”:
Selection of phototrophs:
## [1] 0 47## [1] 314 47## [1] 19412 47#create a table per group and count in how many samples they occur.
Dinophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Dinophyceae"),]
Dinophyceae_tb[1:5,1:5]## TARA_102_SUR_0d2_3 TARA_109_SUR_0d2_3 TARA_110_SUR_0d2_3
## OTU_27905 0 0 0
## OTU_27950 0 0 0
## OTU_28007 0 0 0
## OTU_28206 0 1 0
## OTU_28215 0 0 0
## TARA_111_SUR_0d2_3 TARA_112_SUR_0d2_3
## OTU_27905 0 1
## OTU_27950 0 0
## OTU_28007 0 0
## OTU_28206 0 0
## OTU_28215 0 0Dinophyceae_tb_occur <- Dinophyceae_tb[,1:43]
Dinophyceae_tb_occur[1:5,1:5]## TARA_102_SUR_0d2_3 TARA_109_SUR_0d2_3 TARA_110_SUR_0d2_3
## OTU_27905 0 0 0
## OTU_27950 0 0 0
## OTU_28007 0 0 0
## OTU_28206 0 1 0
## OTU_28215 0 0 0
## TARA_111_SUR_0d2_3 TARA_112_SUR_0d2_3
## OTU_27905 0 1
## OTU_27950 0 0
## OTU_28007 0 0
## OTU_28206 0 0
## OTU_28215 0 0dim(Dinophyceae_tb_occur)## [1] 6 43length(Dinophyceae_tb_occur[,colSums(Dinophyceae_tb_occur) > 0])## [1] 11#Dinophyceae_tb_samples <- Dinophyceae_tb_occur[,colSums(Dinophyceae_tb_occur) > 0]
#length(Dinophyceae_tb_samples[which(colSums(Dinophyceae_tb_occur) != 0)])
Prasinophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "other_Prasinophyceae"),]
Prasinophyceae_tb_occur <- Prasinophyceae_tb[,1:43]
length(Prasinophyceae_tb_occur[,colSums(Prasinophyceae_tb_occur) > 0])## [1] 41Chrysophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Chrysophyceae"),]
Chrysophyceae_tb_occur <- Chrysophyceae_tb[,1:43]
length(Chrysophyceae_tb_occur[,colSums(Chrysophyceae_tb_occur) > 0])## [1] 0Pelagophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Pelagophyceae"),]
Pelagophyceae_tb_occur <- Pelagophyceae_tb[,1:43]
length(Pelagophyceae_tb_occur[,colSums(Pelagophyceae_tb_occur) > 0])## [1] 43Dictyochophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Dictyochophyceae"),]
Dictyochophyceae_tb_occur <- Dictyochophyceae_tb[,1:43]
length(Dictyochophyceae_tb_occur[,colSums(Dictyochophyceae_tb_occur) > 0])## [1] 43Cryptomonadales_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Cryptophyceae"),]
Cryptomonadales_tb_occur <- Cryptomonadales_tb[,1:43]
length(Cryptomonadales_tb_occur[,colSums(Cryptomonadales_tb_occur) > 0])## [1] 31Bacillariophyta_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Bacillariophyceae"),]
Bacillariophyta_tb_occur <- Bacillariophyta_tb[,1:43]
length(Bacillariophyta_tb_occur[,colSums(Bacillariophyta_tb_occur) > 0])## [1] 39Chlorarachniophyta_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Chlorarachniophyceae"),]
Chlorarachniophyta_tb_occur <- Chlorarachniophyta_tb[,1:43]
length(Chlorarachniophyta_tb_occur[,colSums(Chlorarachniophyta_tb_occur) > 0])## [1] 8Bolidophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Bolidophyceae"),]
Bolidophyceae_tb_occur <- Bolidophyceae_tb[,1:43]
length(Bolidophyceae_tb_occur[,colSums(Bolidophyceae_tb_occur) > 0])## [1] 34Pinguiochysidales_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Pinguiophyceae"),]
Pinguiochysidales_tb_occur <- Pinguiochysidales_tb[,1:43]
length(Pinguiochysidales_tb_occur[,colSums(Pinguiochysidales_tb_occur) > 0])## [1] 3Prymnesiophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Prymnesiophyceae"),]
Prymnesiophyceae_tb_occur <- Prymnesiophyceae_tb[,1:43]
length(Prymnesiophyceae_tb_occur[,colSums(Prymnesiophyceae_tb_occur) > 0])## [1] 43Mamiellophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Mamiellophyceae"),]
Mamiellophyceae_tb_occur <- Mamiellophyceae_tb[,1:43]
length(Mamiellophyceae_tb_occur[,colSums(Mamiellophyceae_tb_occur) > 0])## [1] 31Eustigmatophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Eustigmatophyceae"),]
Eustigmatophyceae_tb_occur <- Eustigmatophyceae_tb[,1:43]
length(Eustigmatophyceae_tb_occur[,colSums(Eustigmatophyceae_tb_occur) > 0])## [1] 9Chlorophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Chlorophyceae"),]
Chlorophyceae_tb_occur <- Chlorophyceae_tb[,1:43]
length(Chlorophyceae_tb_occur[,colSums(Chlorophyceae_tb_occur) > 0])## [1] 2Ulvophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Ulvophyceae"),]
Ulvophyceae_tb_occur <- Ulvophyceae_tb[,1:43]
length(Ulvophyceae_tb_occur[,colSums(Ulvophyceae_tb_occur) > 0])## [1] 0Raphydophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Raphydophyceae"),]
Raphydophyceae_tb_occur <- Raphydophyceae_tb[,1:43]
length(Raphydophyceae_tb_occur[,colSums(Raphydophyceae_tb_occur) > 0])## [1] 0Trebouxiophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Trebouxiophyceae"),]
Trebouxiophyceae_tb_occur <- Trebouxiophyceae_tb[,1:43]
length(Trebouxiophyceae_tb_occur[,colSums(Trebouxiophyceae_tb_occur) > 0])## [1] 1Phaeophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Phaeophyceae"),]
Phaeophyceae_tb_occur <- Phaeophyceae_tb[,1:43]
length(Phaeophyceae_tb_occur[,colSums(Phaeophyceae_tb_occur) > 0])## [1] 2Phaeothamniophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Phaeothamniophyceae"),]
Phaeothamniophyceae_tb_occur <- Phaeothamniophyceae_tb[,1:43]
length(Phaeothamniophyceae_tb_occur[,colSums(Phaeothamniophyceae_tb_occur) > 0])## [1] 0Xanthophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Xanthophyceae"),]
Xanthophyceae_tb_occur <- Xanthophyceae_tb[,1:43]
length(Xanthophyceae_tb_occur[,colSums(Xanthophyceae_tb_occur) > 0])## [1] 0Chlorodendrophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Chlorodendrophyceae"),]
Chlorodendrophyceae_tb_occur <- Chlorodendrophyceae_tb[,1:43]
length(Chlorodendrophyceae_tb_occur[,colSums(Chlorodendrophyceae_tb_occur) > 0])## [1] 2IncertaeSedis_Archaeplastida_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "IncertaeSedis_Archaeplastida"),]
IncertaeSedis_Archaeplastida_tb_occur <- IncertaeSedis_Archaeplastida_tb[,1:43]
length(IncertaeSedis_Archaeplastida_tb_occur[,colSums(IncertaeSedis_Archaeplastida_tb_occur) > 0])## [1] 0Nephroselmidophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Nephroselmidophyceae"),]
Nephroselmidophyceae_tb_occur <- Nephroselmidophyceae_tb[,1:43]
length(Nephroselmidophyceae_tb_occur[,colSums(Nephroselmidophyceae_tb_occur) > 0])## [1] 0Pavlovophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Pavlovophyceae"),]
Pavlovophyceae_tb_occur <- Pavlovophyceae_tb[,1:43]
length(Pavlovophyceae_tb_occur[,colSums(Pavlovophyceae_tb_occur) > 0])## [1] 2Rhodophyceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Rhodophyceae"),]
Rhodophyceae_tb_occur <- Rhodophyceae_tb[,1:43]
length(Rhodophyceae_tb_occur[,colSums(Rhodophyceae_tb_occur) > 0])## [1] 0Rappemonads_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Rappemonads"),]
Rappemonads_tb_occur <- Rappemonads_tb[,1:43]
length(Rappemonads_tb_occur[,colSums(Rappemonads_tb_occur) > 0])## [1] 37MOCH_1_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "MOCH-1"),]
MOCH_1_tb_occur <- MOCH_1_tb[,1:43]
length(MOCH_1_tb_occur[,colSums(MOCH_1_tb_occur) > 0])## [1] 0MOCH_2_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "MOCH-2"),]
MOCH_2_tb_occur <- MOCH_2_tb[,1:43]
length(MOCH_2_tb_occur[,colSums(MOCH_2_tb_occur) > 0])## [1] 0MOCH_5_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "MOCH-5"),]
MOCH_5_tb_occur <- MOCH_5_tb[,1:43]
length(MOCH_5_tb_occur[,colSums(MOCH_5_tb_occur) > 0])## [1] 0Prasinophyceae_clade_VII_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Prasinophyceae_clade-VII"),]
Prasinophyceae_clade_VII_tb_occur <- Prasinophyceae_clade_VII_tb[,1:43]
length(Prasinophyceae_clade_VII_tb_occur[,colSums(Prasinophyceae_clade_VII_tb_occur) > 0])## [1] 0Prasinophyceae_clade_IX_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Prasinophyceae_clade-IX"),]
Prasinophyceae_clade_IX_tb_occur <- Prasinophyceae_clade_IX_tb[,1:43]
length(Prasinophyceae_clade_IX_tb_occur[,colSums(Prasinophyceae_clade_IX_tb_occur) > 0])## [1] 0Pyramimonadaceae_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "Pyramimonadaceae"),]
Pyramimonadaceae_tb_occur <- Pyramimonadaceae_tb[,1:43]
length(Pyramimonadaceae_tb_occur[,colSums(Pyramimonadaceae_tb_occur) > 0])## [1] 11other_plastids_tb <- tb16_protists_non.norm[which(tb16_protists_non.norm$class_A == "other_plastids"),]
other_plastids_tb_occur <- other_plastids_tb[,1:43]
length(other_plastids_tb_occur[,colSums(other_plastids_tb_occur) > 0])## [1] 29## [1] 43## [1] 43## reads_per_class OTUs_per_class
## Bacillariophyceae 1777 168
## Bolidophyceae 312 7
## Chlorarachniophyceae 33 5
## Chlorodendrophyceae 2 2
## Chlorophyceae 2 2## reads_per_class OTUs_per_class samples_per_class
## Prymnesiophyceae 55897 50 43
## Mamiellophyceae 32273 15 31
## Pelagophyceae 11504 10 43
## Cryptophyceae 3872 28 31
## Dictyochophyceae 2954 7 43
## other_Prasinophyceae 2694 26 41
## Bacillariophyceae 1777 168 39
## Bolidophyceae 312 7 34
## Rappemonads 249 4 37
## Pyramimonadaceae 147 7 11
## other_plastids 93 28 29
## Chlorarachniophyceae 33 5 8
## Dinophyceae 25 6 11
## Eustigmatophyceae 25 2 9
## Pinguiophyceae 3 1 3
## Chlorodendrophyceae 2 2 2
## Chlorophyceae 2 2 2
## Phaeophyceae 2 2 2
## Pavlovophyceae 2 1 2
## Trebouxiophyceae 1 1 1## reads_per_class OTUs_per_class samples_per_class
## Prymnesiophyceae 55897 50 43
## Mamiellophyceae 32273 15 31
## Pelagophyceae 11504 10 43
## Cryptophyceae 3872 28 31
## Dictyochophyceae 2954 7 43
## other_Prasinophyceae 2694 26 41
## Bacillariophyceae 1777 168 39
## Bolidophyceae 312 7 34
## Rappemonads 249 4 37
## Pyramimonadaceae 147 7 11
## Chlorarachniophyceae 33 5 8
## Dinophyceae 25 6 11
## Eustigmatophyceae 25 2 9
## Pinguiophyceae 3 1 3
## Chlorodendrophyceae 2 2 2
## Chlorophyceae 2 2 2
## Phaeophyceae 2 2 2
## Pavlovophyceae 2 1 2
## Trebouxiophyceae 1 1 1## reads_per_class OTUs_per_class
## Cyanobacteria 400768 364
## other_bacteria 3171424 23955
## NA NA NA
## NA.1 NA NA
## NA.2 NA NA
OTUs per class vs. samples in which they occur - PROTISTS vs. CYANOBACTERIA [PLOT DESCRIPTION]
## reads_per_class OTUs_per_class samples_per_class
## 100.000 100.000 1013.953## reads_per_class OTUs_per_class samples_per_class
## Prymnesiophyceae 1.090584e+01 7.0621469 100.000000
## Mamiellophyceae 6.296655e+00 2.1186441 72.093023
## Pelagophyceae 2.244499e+00 1.4124294 100.000000
## Cryptophyceae 7.554503e-01 3.9548023 72.093023
## Dictyochophyceae 5.763430e-01 0.9887006 100.000000
## other_Prasinophyceae 5.256155e-01 3.6723164 95.348837
## Bacillariophyceae 3.467033e-01 23.7288136 90.697674
## Bolidophyceae 6.087306e-02 0.9887006 79.069767
## Rappemonads 4.858138e-02 0.5649718 86.046512
## Pyramimonadaceae 2.868058e-02 0.9887006 25.581395
## Chlorarachniophyceae 6.438497e-03 0.7062147 18.604651
## Dinophyceae 4.877649e-03 0.8474576 25.581395
## Eustigmatophyceae 4.877649e-03 0.2824859 20.930233
## Pinguiophyceae 5.853179e-04 0.1412429 6.976744
## Chlorodendrophyceae 3.902119e-04 0.2824859 4.651163
## Chlorophyceae 3.902119e-04 0.2824859 4.651163
## Phaeophyceae 3.902119e-04 0.2824859 4.651163
## Pavlovophyceae 3.902119e-04 0.1412429 4.651163
## Trebouxiophyceae 1.951060e-04 0.1412429 2.325581
## Cyanobacteria 7.819223e+01 51.4124294 100.000000
Reads per class vs. OTUs per class:
Reads per class vs. samples in which they occurr:
